So let's see...
you got an archive with an iso and a cur file where -due to a datfile update- the cue file becomes unneeded (different hash). So cmpro's unneeded check will remove it.
Then you got the correct cue file for it somewhere...and want that to be added to the 7z.
Well, there are 2 ways...
Scanner's fix missing:
This method mainly checks (besides your backup folder and other sets in your romfolder) the setup addpaths for files which are missing your rompaths. It looks there by a setname compare...so if you got the right cue file in an addpath, it needs to be in a folder or archive with the correct setname.
Rebuilder (which is also used when you drag'n drop files into the scan results tree window):
The rebuilder doesn't care about names. It takes anything you drop in (or got as rebuilder source). If it's an archive, it looks at each file inside it. It only compares hashes and if a hash is matched against anything in the currently loaded datfile, it adds the file to the given destination and uses the correct name there.
So basically, the rebuilder is an adder.
So...for your bin/cue file example: Either simply drag'n drop the right cue inside the scan tree window (rebuilder destination points to your collection / rompath or be sure you got the right cue in a correctly named folder in an addpath.