For some reason although we're extending trap doors, BYG trapdoors destroy the block above it "sometimes."

You are using the TallBlockItem type for your Trapdoor Items. TallBlockItem sets the BlockState of the block above where you set it to the default for air, and since trapdoors are single blocks they pass the check to see whether they can be placed to begin with.

Fairly sure that if you change it to use a BlockItem you won't have the issue.

Thankyou! You we're correct that did fix it. Silly mistake on our part.