With two OS’s on separate disks, and with separate bootloaders, you should be able to do anything to either OS without affecting the other.
If you are unsure, unmount the disk that is not being used.
You do not say anything about backups.
I hope you have some sort of system backup to an external disk? If not make backups before you do anything.
Clonezilla is a simple tool to make backup images of all your disk partitions.
Regards
Neville