as I said, I do see a possible need in a "fix this <selected item>" option....it's added to my wishlist already
Rebuilder is file based, ie it doesn't know about sets or better about complete sets.
It takes a file from the source and creates all instances of that hash match in the destination. If a file is shared in 1000 sets, you get the file added to such 1000 sets (even if it's the only match).
Generally Scanner/Rebuilder/Merger work on active sets...in Set-Information you can limit the number of active sets in various ways (e.g. regular expressions, via manual enable/disable, via lists, via 'avail sets' button or variable usage etc).
Actually the "delete->all listed incomplete sets" should do what you want...Selected after a scan (!) which lists the incomplete sets it runs through all rompaths and removed the ones which are listed as incomplete. Be sure to have "sets" enabled during the scan.
Please retest this.