When updating the working copy from one commit to another, I didn't think we would delete files that were not untracked in the first commit. I suspect the files are actually still available in the repo, but we'd appreciate a bug report if you can reproduce the problem.

The other issue you ran into with ignored files becoming tracked is a known limitation. I agree that it's really annoying. We have talked about it many times before but we didn't have a proper issue for tracking it, so I created one now: https://github.com/jj-vcs/jj/issues/5596