I see now about the schnapps issue, it might be related to schnapps experiencing trouble when trying to export
but I cannot be sure, neither whether this may not happen with more contemporary versions of the OS. Unfortunately schnapps does not offer to exclude certain paths [1]
There is no easy debug option for schnapps and it would require other tools, e.g. strace, to take a closer look.
Alternatively, since medkit being just a compressed archive, it should be possible to generate one with common archiving tools such as tar.