It sounds like git thinks that the missing files were deleted on the master at some point between where it branches from dev and the pre-merge head. That’s the only reason I can think of for why git would silently drop tracked files during a merge.
Unfortunately, I don’t know a good way to fix that. I’d probably just re-add all the deleted files from the dev branch manually (or with a little bit of bash scripting), and then to a git commit --amend to revise the merge commit to include them.