No, it's not normal to do a full copy after a profile modification - plus, there's no setting to force it to re-copy a file that is listed as present both sides (and matching). This assumes the Destination is 'static', of course (if it has a Variable such as %DATE% in it, it might be creating new (empty....) Destination paths every run, for all I know)
Sounds like you may have accidentally changed the Destination so that it is backing up to a (very similar but slightly different) path now. A backup that takes longer than expected (because it's copying everything - again) but has files missing where you look/expect is symptomatic of copying to one place and looking in another.
Try right-click profile > Open Right/Destination and see if all your files are there? That's where the profile is pointing (and assuming it contains no Variables) was pointing last run.
Check the logs - are the 'missing' files listed? If so, they were copied somewhere...if not, they may have been Excluded (accidentally)
Sounds like you may have accidentally changed the Destination so that it is backing up to a (very similar but slightly different) path now. A backup that takes longer than expected (because it's copying everything - again) but has files missing where you look/expect is symptomatic of copying to one place and looking in another.
Try right-click profile > Open Right/Destination and see if all your files are there? That's where the profile is pointing (and assuming it contains no Variables) was pointing last run.
Check the logs - are the 'missing' files listed? If so, they were copied somewhere...if not, they may have been Excluded (accidentally)