The game doesn't seem to use Update.esm... If I enable it, it's disabled the next time I open the data file selection
The game automatically loads the update esm, there is no need to check it.
Thanks! Actually I just discovered CK can do it by selecting it, and hitting the delete key. The old CS coundn't do that. I've not tested the plugin yet though.
The problem is that the udpate esm contains updated information for game mechanics, quests etc. So if you change existing gameplay you may end up breaking stuff without even knowing it if the esm is not loaded. I realized this while working on an enchantment overhaul. The magic effects for restore/regenerate health/magicka/stamina are lacking important keywords in the Skyrim esm which were added by the update esm. I altered those effects and some perks didn't work anymore afterwards. The reason was that my changes were done to the entries in the Skyrim esm so my plugin saved them without the keywords. That's just one example, there are more changes in the esm of course.
I'd rather load the update esm before you run into problems you didn't know of since you couldn't see them when you made your mod. Only mods that add 100% new content and don't alter existing stuff don't need to do this.