I have special branch (release branch) which is an exact copy of master branch with some files and directories removed. No development is happening on this branch, however i
There's probably a better way to do this, but I solved a similar problem by doing the merge (with the default merge strategy) and then running
git status | grep 'deleted by us' | awk '{print $4}' | xargs git rm
After this, you should resolve other conflicts as normal and then commit.
This just deletes all files that had been deleted on the current branch, which I think is what you want.