System restore data is drive-specific. This means that you cannot transfer restore data between drives. I don't use system restore because it's a safe haven for malware.
If you open up the system restore tab in the system properties, it will show it for all the drives it's monitoring. If your 'slave' drive is listed in there, then it will delete the data when you turn it off.
You could also use system restore to delete all but the most recent restore point, or use a program like CCleaner to delete the excess data.