I think the main questions here are:
1) did you install a totally new OS on the 'master' drive?
2) are you in a dual-boot situation?
IF the slave drive isn't used to boot from, then most likely
it is safe to delete the Windows folder from the slave drive. In other words, it's being used just as a data drive.
Given that you are uncertain however, then for maximum safety I strongly recommend you make a FULL system backup of BOTH the slave drive AND the master drive, then
delete the Windows folder on the slave drive.
If ALL your key applications continue to work the way you expect them to (and you should try all the programs you use), then you're good to go. If something major goes wrong, then you restore the backup images to the respective drives. Having the backups protects your OS, your applications, and your data.
The reason I don't say simply copy the slave drive Windows folder and then delete it, is given your uncertainty, there may be associated files on the slave OR master drive (e.g. registry, settings, shortcuts, data) that could be irreversibly changed if an error occurs when you try to run certain programs. If you DON'T have full disk backups of BOTH drives, then you will be unable to restore your system to its original state
If you DO have full backups of both drives, then no matter what happens you can always return to your exact current system state and no harm no foul.
It boils down to the degree of risk you're willing to take. Personally, I'm VERY conservative in this regard.
I can highly recommend either Macrium Reflect Free Edition or DriveImage XML to backup your disks. Both are freeware, reliable, and easy to use. Having full system bacukps has saved me valuable time and data multiple times over the years.
However, you do of course have to have somewhere else (not on either of the two disks) to store your backup image files, and they will be large files. With both backup programs, you can either create an emergency 'rescue' boot CD/DVD and use the rescue disc to restore your disks, or you can restore your disks using a second machine running Windows.