Welcome to discussions!
I swap out one of my HDs each day to send off site. As long as we remember to unmount it first with Disk Utiltiy, it's fine. If we forget, the server will panic. Last time it happened to my assistant, I could hardly keep from laughing!
On my machine, the left drive is the root drive, the middle is a clone which stays there, and the right drive is a clone that gets sent offsite. Each morning, after checking the logs to make sure things are okay, we run an asr based script to clone the root drive to each of the others, then unmount the right one (it could be one of three drives that are in rotation for this, two would be enough but in the winter months I'd rather let the drive warm up before inserting it and I had an extra just laying around) and pull it out and insert the next right drive. It will mount automatically. Except for the paper work, that's it.
Roger