Hi!
Your explanation is surely clear. I definitely didn't think about this eventuality, so it will be surely fixed in a next version.
For the moment, I think you should try splitting the file (after making a copy, to be sure), like you said, and then process each fragment separately. If you happen to get only a piece of some bitmaps that where just in the mid of a split position, you can then subsequently try with a different number of parts / different size.
For splitting the file, you can check this article:
Technobuzz.net - 8 ways to Split Large FilesHope this helps,
Bye!