How do you do this? I've updated version 1 of my mod (basically just made changes to the original in my Data folder - but still have a copy of the original elsewhere) and then made a copy of it and renamed it version 2. If I run the game with the just the new version 2 the active .esp in the Data Files and then load a very old save or start a brand new game the quest and the mod function correctly - as you would expect. However if I load my most current save it is expecting to find version 1 of the mod as the active esp, consequently the mod doesn't work and all the data files are ignored.

As there is no "Save As" option in the CK and renaming is only possible by renaming the actual .esp file - how do I make version 2 compatible for other players who are already using version 1 of my mod and have saves?

The only work around I have at the moment is leaving the .esp file name the same as version 1 - which might cause a little confusion but at least it works with current saves, players only have to remove a few items from Hjerim House before using it and it'll just update without issue but remains with the version 1 name.

If you change the name of a plugin, the game sees it as an entirely new plugin. There is no other way for it to work. I keep my versions numbered while I am working on them and then change the name to the original before I test or post them.

I made the mistake of putting the version number in the plug-in name, in hindsight I shouldn't have done.

No - you can't really do that. It will need to be there forever. I feel your pain.