The title of this thread demonstrates a common misconception about such Elections/Nominations.
It is only if the taxpayer has two (or more) RESIDENCES not PROPERTIES, then an Election is competent. Therefore, any purported Election (even if lodged with HMRC) may be invalid.
It appears from the details given that House A (the "old house") is likely to be your residence from 2000 to 2011.
However, since you seem to want to "retire" back in House B, it is the possible CGT liability on the disposal of House B which is of current concern?
You have identified the two possible options of CGT mitigation - PPR (Principal Private Residence) Relief or Entrepreneur Relief. Of the two, the latter is likely to be more advantageous. Although House B may have been a Holiday Let, did it actually qualify, in tax terms, as a Holiday Let.
What is the estimated gain on House B, as it is only 4 years old?
What is the reference to the Title Deeds by your old accountant? Is only House A registered at the Land Registry?
To try & answer your questions :
1. You can ask HMRC if they hold the relevant Election(s) sent in my your old accountant. I would not advise it at this stage, but wait until all the data is assembled.
2. Possibly - but refer to my above comments.
3. If no Election was lodged with HMRC, you may have a negligence claim against your old accountant or the new accountant (depending on the terms of the merger). A Late Election MIGHT be accepted by HMRC, as a concession
Have you read HMRC's Help Sheet HS283 on this subject?
[For disposals after 5 April 2014, the exemption for the last 36months of ownership is reduced to 18 months.]