Well what-do-ya-know. I didn't know you could do that. I thought once you went back to un-safe you wiped out your safe side. I thought that was what that warning was all about when you try it (thats why I didnt). I didn't know you could flip-flop back and forth willy-nilly.
Sure you can do it. Haschode's original intention with SS was for developers to be able to have a stable (non-safe 'to screw with" side) ROM and have the safe side as a place where ROMs could be flashed for testing purposes. The /system of each ROM (non-safe/safe) is not backed up when swapping modes, only the data. This is because he uses the normal /system partition for the non-safe side and the /preinstall partition for the safe side. When you swap modes in recovery, is where the trickery goes on. The recovery mounts the original /system as "systemorig" and mounts /preinstall as /system if you are booting into safe side instead of the normal /system. The data for each is backed up to internal storage when swapping modes and restored according to which mode you are swapping to. This is the one area that some people have trouble with, since there is kinda limited space on the internal emmc, sometimes there isn't enough room for the backup and the swap may fail to in the backup process, that means that when you swap back, there will not be any data to restore. To avoid this, I always make sure there is plenty of room in internal storage and also usually make a manual backup to the external storage when swapping modes, just in case something goes wrong, though I have never had to use it.
I realize that's probably way more information than anyone wanted to read, but I was on a roll.