I'll be facing the same issue myself in the near future, having moved in four years ago and taken my time finishing things off sufficiently to get a completion certificate.
This recent tribunal case is extremely helpful: http://financeandtax.decisions.tribunals.gov.uk//judgmentfiles/j11202/TC07240.pdf
I don't know whether HMRC is appealing, but if they don't (or they do and they lose), this case represents the end of HMRC's vendetta against those who move in before obtaining a completion certificate.
I'd recommend reading the entire case, but the most relevant points are here:
42. From the statutory wording, the Tribunal finds that the meaning of ‘completion’ under reg 201(a) is to be given the plain meaning as referential to a certificate of completion for the following reasons:
(1) Applying the ordinary rules of statutory construction, the plain meaning of ‘completion’ under reg 201(a) is to be defined by the issue of a certificate of completion under reg 201(b)(i). It is a clear-cut definition for ‘completion’ that enables the claimant and the Commissioners to establish the common ground, and for the efficient administration of the refund scheme so that there is no cause for ambiguity or dispute such as the present case.
(2) The primacy given to a certificate of completion is evident in the statutory wording; it is the sine qua non for the purposes of a VAT refund claim under the DIY Scheme. The statutory wording makes it clear that the preferred document is a certificate of completion, and it is only in the absence of which that the alternative should be provided in substitution.
(3) It is only in the absence of a certificate of completion that the Commissioners would entertain a claim based on the alternative. What is satisfactory as an alternative is not specified by the statute in like manner as a certificate of completion. HMRC’s guidance notes in relation to question 14 of the claim form then come in to fill the gap.
(4) ‘If you do not have a Completion Certificate yet, we will accept one of the following documents’, states the guidance notes (see §7). From the word ‘yet’, it can be inferred that the alternative documentation is one that can be obtained before the house builder is able to obtain a completion certificate. In other words, the alternative documentation to a completion certificate has the effect of enabling the house builder to bring forward the claim ahead of the issue of a completion certificate.
(5) Per the guidance notes, the alternative documentation that is satisfactory to the Commissioners are: a habitation letter or a Joint valuation Board Notice of Tax Banding (Scotland); a VOA (England and Wales); a District Valuer’s Certificate of Valuation (Northern Ireland); or a letter from a certified lender in relation to a loan secured on the new-build.
(6) The alternative documentation is to serve as evidence of completion, to enable a claim for a VAT refund to be made before a new build has obtained its completion certificate.
(7) The provisions under reg 201(b)(ii) to (v) concern the validity of the input VAT being claimed, by reference to the valid invoice from a registered supplier, in relation to the goods being imported, and in relation to whether the goods so claimed are genuinely used in the making of the supply of a new dwelling. None of these provisions pertain to the meaning of ‘completion’ for any further possible meaning of completion to be drawn after reg 201(b)(i).
43. In conclusion, the statutory interpretation of reg 201(a) is that ‘completion’ is referential to the issue of a certificate of completion. For the purposes of a VAT refund claim under the DIY Scheme, the only definition in terms of ‘completion’ is by reference to the documentation stipulated to evidence completion under reg 201(b)(i).
44. The stipulation cannot be clearer; it is either by way of ‘a certificate of completion obtained from a local authority’ or by alternative documentation as specified in the guidance notes. The proof of ‘completion’ for the purposes of reg 201 is by way of documentation, and documentation alone.
45. There are no extraneous definitions to the meaning of ‘completion’ within reg 201 that can be extracted from the statutory wording as pertaining to the date of occupation, or to the date of the last invoice being included in the claim. We therefore reject both of HMRC’s interpretations of ‘completion’ as without any basis in law.
46. It is plain from the statutory wording that a bright-line definition is to be given to ‘completion’ by reference to the stipulated documentation alone. The definition of ‘completion’ is not to be founded on circumstantial factors, which are in turn subject to different documentation to establish. The date of occupation, or the date of last purchases are not provided as possible alternative points of completion in the statute, not to mention that these are facts that need to be established by evidence that has no reference in the statute whatsoever.
47. If two different dates of completion as reckoned by HMRC were indeed possible according to the statute, then the relevant provision would seem to us flawed in its conception because: (a) it would promote ambiguity in establishing ‘completion’ subject to arbitrary documentation as evidence, and (b) it would allow such wide margin of difference, with the range of some 8 years between the possible date of 23 December 2008, and a later date of 2 June 2016. Such ambiguity and wide margin in establishing ‘completion’ cannot be desirable in providing for an efficient scheme for administering refund, and cannot be the intention of the legislature.
The purpose of the DIY Scheme
48. The literal interpretation that ‘completion’ in reg 201 has to be given a clear-cut definition as referential to the date of a completion certificate alone is further supported by a purposive construction of the provision.
49. The supply of new dwellings is a zero-rated supply. For this reason, a VAT registered developer in the business of building new dwellings can apply for a zero rated certificate so that no VAT is borne on the purchase of materials for building new homes. On a purposive construction of reg 201, a VAT refund is to compensate a DIY house builder for the input VAT he has borne in making the self-supply of a new dwelling, and to put him in the same position as a developer who is VAT registered.
50. Regulation 201 is a mechanism to give effect to the EU principle of fiscal neutrality, so that a DIY house builder eventually can obtain the supply of a new build dwelling at zero-rate.
52. On a purposive construction of reg 201, we reject HMRC’s interpretation that the date of completion can be arbitrarily set as the date of occupation: ‘Usually a property isn’t occupied until it is complete’ (per ADR exit document). Not only is this interpretation non-permissible as a matter of statutory construction, but in the context of the DIY Scheme, it is not unusual that a DIY house builder starts to inhabit the building while works continue towards completion. For reasons as those related by Mr Farquharson, it is not uncommon for occupation of a new dwelling to take place before its ‘completion’ to plan; reasons such as to save the costs of running and renting an alternative home, or to take care of the property in its continual course of construction. In the present case, the occupation was the garage in the first instance anyway, and not of the main house.
53. We also reject HMRC’s interpretation that in the alternative, the date of completion should be set as the date of the last invoice being included for the refund. In B Bowley v HMRC  UKFTT 0683 (TC), the appellant’s VAT refund claim was allowed, where the planning permission was granted in July 1982 and the completion certificate in June 1994. In the context of a DIY new build, construction often happens in bursts of activity, punctuated by periods of inactivity, as was in Bowley and in the present case. The timing of an invoice is often dictated by when funds become available for a purchase.
54. The date of the last invoice cannot be determinative as the date of completion, since the timing of when to draw a line by triggering ‘completion’ in the meaning of reg 201 is for a house builder to decide. It is reasonable to assume that in the normal course of event, a house builder will make a claim at the earliest possible juncture for cash flow reasons. It is then for a DIY house builder to decide when that earliest possible juncture should be, since by precipitating ‘completion’ through obtaining the relevant documentation, a DIY house builder is effectively foregoing the opportunity of making any future claim of what may turn out to be legitimate expenses as a matter of fact
55. In the instant case, if Mr Farquharson had stayed on in the new-build as he had intended to be his permanent home, he would have incurred further expenses in completing the dwelling to the original plan. From the photographs shown, we find seven rooms were incomplete in so far as a developer building a new dwelling to sell on to a home owner would not have been able to sell the property in that state as being ‘complete’. To that extent, HMRC have noted in the ADR exit document that one bathroom had no plumbing in place: a developer simply cannot sell a dwelling with a room specified as bathroom without any plumbing, let alone other essential features and fixtures required to make a room a bathroom, which were absent as noted above.
56. Mr Farquharson was in the invidious situation of not knowing whether he should precipitate the issue of a completion certificate, thereby foregoing any further claim of VAT refund on costs in completing the house to the plan (if he were to be required to do so) in order to sell the house.
57. As a matter of fact, the issue of the Certificate of Completion in the present case was brought forward before the dwelling was fully completed in order to make the sale of the house possible. In the final analysis, the incoming owner of the property who would have to complete the building works which would have qualified for the DIY Scheme, would no longer be able to make any claim for the input VAT borne in completing those unfinished rooms.
58. Finally, we need to highlight the arbitrariness of HMRC’s own interpretation by reference to invoice dates. In the review conclusion letter, HMRC stated that ‘the building is a fully functioning dwelling and that any remaining work is of a cosmetic or minimal nature’, which is to say that the remaining work is of a nature that is ‘postcompletion’. In the ADR exit document (and at the hearing), HMRC somehow seem to have conceded that the invoices in May 2016 in relation to ‘decorative materials’ before the sale of the house were ‘pre-completion’ for setting the completion date as immediately after these invoices. If the May 2016 invoices were for ‘decorative materials’, then the invoices were ‘of the cosmetic and minimal nature’ that should have been ‘post-completion’. The inconsistency within HMRC’s own interpretations is indicative of the arbitrariness of the respondents’ approach. To describe the ‘remaining work’ as of ‘a cosmetic or minimal nature’, while noting from the sales brochure that one en-suite bathroom had no plumbing seems to us, not only arbitrary, but a travesty in semantics. HMRC’s interpretation of completion by reference to the date of last invoices has no statutory basis; is self-contradictory; and is contrary to the principle of legal certainty.