WOW ,it is funny you said that. Because it is kinda true.
If you don't backup a custom style it will be hosed if you try to just ftp and copy the css file back up to the server.
So you need to use the export /import utility in the cp to make them work again. Not a full backup but a style export.
Then if you need to restore a site after all the uploads you need to import your style.
Kinda forgot about that quirk.
Just making a restore from a backup with say ftp does not work.
