Start again !!!
I suggest you download WinMerge from SourceForge.
You aim at two targets - the two points on each drive to be compared.
It compares every file in each designated directory, and all their sub-directories.
Comparison is quick - e.g. 1 minute for 40,000 files on my Drive C:\ w.r.t. Drive L:\ using File size comparison - similar time using file date option, or a coffee break using a detailed examination of every byte in every file (that gives it 7 GByte to read !!!).
The results appear with one file name per row and :-
If it matches between both targets,
If it is different between both targets, or
Which target it is unique to.
Normal use is to click on any row, and a file comparison shows you all the differences between them.
You do not have to use the built in file comparator.
You can simply copy what it has found different to any other location for any sort of independent processing by your preferred tools.
e.g. you can rapidly select all desired files/subdirectories of one target, and either copy them or move them to the other target, or even to a totally different choice on another drive, where what you desire can be unique, different, or identical - you can even mix and match.
Regards
Alan