Thats all mixed up!!
How have you got the drives setup? if you want to use them like this then your smaller drive should be your boot drive set as Master and have the OS and main applications installed, the second larger drive ideally needs to be a blank canvass, nothing on it at all, just a clean formatted drive, with nice neat labelled folders for all your stored music/pictures and work.
Note* this makes sense as long as both drives are of similar speeds (no point in making an old slow drive as your main boot drive)
If you have enough space on the smaller drive I would make a folder and use explorer to temperarily transfer the files you want to save into it, once you have copied across everything you want to save you can format the larger drive leaving it in a clean virgin state.
Then just copy back over your saved data, job done.
Martin
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