moving large amounts of data into new folders after back up

Hi guys, I'm a little unsure on how to progress with something and would like some advice if possible?

I've backed up about 500 gigs worth of files, to a second drive. I've then mirrored that backed up drive to a Google Drive account, which took about 5 days to finish.

The problem is, it has become necessary to completely rearrange the folder structure for these files on the source drive. None of the files themselves have changed, however they are all now in completely different places.

Is there a backup method I can use that won't now necessitate re-uploading all of the files once again?

Thanks in advance for your time