I think you should do it in 1 update because it would as you have said break mod compatibility. I personally have 200 mods and waiting for them all to update would mean a very long wait indeed.
Or that you could add in the option to stay on the currect version of the game through the "betas" feature for at least a few weeks while mods are updated and release it in 2 updates.
Or that you could add in the option to stay on the currect version of the game through the "betas" feature for at least a few weeks while mods are updated and release it in 2 updates.