I wonder if they've got files tracked by git-lfs. `jj` doesn't handle those yet.
for me, squash merges are enforced on github, and usually results in some weird / empty commits if i rebase a local stack after pulling in changes with part of the stack merged.
It’s also possible that I start my next task without remembering to create a new diff first. That might explain the conflict when the original commit becomes immutable?