there is no problem with un-installing and re-installing EET_end even during playthrough. For example if you need to install some other mod or change install order or whatever else you need to do, uninstalling EET_end in order to do so won't cause any issues. Of course adding mods during playthrough is always risky (because usually you need to install them before you visit area that the mod affects) but this has nothing to do with EET_end.
let me guess, "out of bounds" errors during spell patching like this. It's currently unknown why mods tend to corrupt spells mentioned in the linked topic, but the same is true for vanilla BG2:EE. I would wait before starting large installation until mods that are known to cause it are fixed.
you're right haha. got stucked at SCS quite a lot of times, one of the reasons for the first few resets.
it's painful man that the moment you see the error message at the EE mod setup you have to unsintall and deliete and redownload everything!