Removing a song doesn't actually remove the song.
Hello!
Smart backup in CopyTrans will automatically update your previous backup. Please, try to run the backup again in the same folder!
If the issue persists, please reach out to copytrans@copytrans.net with your log files for support! Here is how to generate them: https://www.copytrans.net/support/preparing-log-files-to-contact-support/
We will be glad to help!
Best regards
CopyTrans Team