If you just converted the main ape file (disc image file) from High to Normal the cue file is as good as before.
If you are speaking about the already imported cue tracks I guess Auto-Import could do something wrong if you have set it to update for external changes and the main file changes. I wouldn't recommend having that option enabled if your library has imported cue tracks.
If you are speaking about converting imported cue tracks to separate track files, it does not work if you have MC set to update the library in the conversion options. The Playback range field is not emptied as it should. The resulting converted files in the library will be unplayable (except the first track because its playback range is still valid). The only way to fix this is to import the files as new library entries after renaming them or changing the file location outside MC.
MC 12 is finally able to correctly convert cue tracks to separate track files and also tag the resulting files. However, this playback range bug has not been fixed.
Is this a known issue?
I don't know.
I discovered the problem and reported it a few months ago, but I don't think anyone has mentioned it since then. I hope it will be fixed in the next MC version.