If the declaration was made this month DHL should contact HMRC to make a post entry amendment, if not then yes advise HMRC of the error made by DHL. Irrespective of which scenario still give DHL a hard time, if pre-entry, you gave them your TURN (Trader Unique Reference Number) - Effectively your VAT number then its their mistake (however have you notified HMRC that you intend to do Imports? If you have then all is good, but if you haven't then maybe that's why they didn't use it. They should have come back to you but probably decided to save time, they would just do the declaration and leave you to sort the mess).
Strictly speaking you should have notified HMRC that you intended to do commercial imports
You can still claim the VAT back but must keep evidence that you have paid it in the first place. This evidence would be the invoice DHL sent you and your bank statement showing the payment.
For future imports maybe either get another shipping agent to act for you, or make sure that you advise DHL (or other fast parcel operator) in advance in writing\email.
Good luck
Thank you for detailed reply, I have contacted HMRC online and after couple of weeks they come up with following response.
"
Thank you for your enquiry of 14 December 2017, regarding the above subject.
Unfortunately the written enquiries team cannot issue C79 certificates.
The VAT Microfilm unit keep copies of all monthly issued certificates for up to 6 years. You can request a replacement of lost or missing certificates from:
HMRC
VAT Central Unit Microfilm Section
8th Floor
Alexander House
Victoria Avenue
Southend-On-Sea
SS99 1AU
You must make your request on business headed paper quoting the VAT registration number and EORI number and month(s) for which replacement is required.
Section 8.10 of VAT Notice 702: Imports contains information on requesting a duplicate C79. "
Now I am not not sure of few things, what do they mean by duplicate C79, I never applied for original in first place.
secondly you said I can still re-claim ? Yes I have invoice for DHL and evidence of my account where money was actually paid into DHL account ?