We have a similar migration tool we built a long time ago, and this project has a bug that we had to address.
When you have to branches that each have a migration, you end up with 2 copies of N_N+1.sql, or worse yet, things that subtly merge w/o error, meaning you have committed migrations that might not run. Or the conflict-resolution process cascades painfully as you "re-sequence" your migrations.
We ended up moving to a solution based on a manifest file; there is a single migrations.json that enumerates the exact order in which migrations must be applied. It causes merge conflicts whenever you have migrations that need their "application order" resolved, and it's fixable just by re-arraning the manifest; no file renaming required. It's been pretty robust so far.