I would highly recommend not editing your existing source as you’ll duplicate everything without a easy way to fix it. I would either make a new source for the system mount and then remove the original source telling Kodi to remove everything from that source from your library or just skip messing around with your sources entirely and just use a path substitution.
Now that the issue appears to have gone away have you tried replaying the same files that had issues to see if the problem was actually the files themselves?