Wrong conflicts on file splits

I keep running into this problem, is there anything I can do to make it better? I'm using stgit but this is a problem in git itself.

I have a patch that splits file A into two files, A and B. Now I merge with another tree and bring in a one line fix to A. The fix touches the pre-split file A in a section that is going to end up in B. Next I re-apply the patch that splits A into A and B.

This results in a large conflict in the post split file A. And no patch being applied to file B which is where the fix belongs.

Repeat this process with a multi-line fix and the whole automated merge process breaks down and I have to carefully figure everything out by hand.

The merge process seems to be unaware of the newly created file B. No patches or conflict ever end up in it.