How to deal with git apply-mailbox conflicts when reconstructing a repo

I'm reconstructing a small repo from scratch in a fresh, empty git repository, using only patches (generated using format-patch -M -B --root master, about 180 patch files in total), and at a point开发者_JS百科 during which a merge conflict occurred in the original history, the patches stop applying. I'm wondering what the rationale behind this is, and how to resolve it, either during the patch generation or application process. I've used the --reject option in git am, and I can manually fix up the rejected hunk, but I know that there are more merge conflicts, and that manual intervention will quickly become unworkable. It seems to me that a complete patch series applied to an empty repo should introduce no conflicts or errors, but perhaps I haven't thought this through.