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.

-- 
Jon Smirl
jonsmirl@gmail.com