With OBMM, so far as I know you'd have to uninstall the package and reinstall the new one. In any case you don't need to go hide out in a test cell.
What I've typically done with OBMM is create a new omod with the update (different version number, obviously), install it, only overwriting those files that really should be overwritten (i.e. don't overwrite resources from mods that you want to prioritize), then after exiting OBMM just remove the old version's omod from the OBMM/mods directory (rather than actually uninstalling it - just remove the omod). Obviously if you need to actually remove resources, rather than selectively overwrite, a more formal uninstall is required.
This process has always worked OK, but I keep meticulous notes about proper install orders. If you're doing it that way you really need to be conscious of what should and shouldn't be overwritten and it can get tedious.
That all said, if I had to do a fresh install of all my mods I would almost certainly use BAIN. I wasn't really aware of it when I started out and since I have 200+ mods installed with OBMM that are comfortably working with each other I'm not really interested in switching at this point just to install updates.