I'd like to switch from Deadly Combat to Ultimate Combat for my next char, which means I should uninstall DC which has scripts. The problem is that I have an ongoing char that I'd like to continue with for a while as well. Which is the safest way to get rid of DC? Should I just uncheck the esp and keep the scripts? Or is best to uninstall everything? What is the worst thing that can happen with my ongoing char if I suddenly remove DC and its scripts?

You can probably do it, if you use a mod manager that uses profiles. Basically use one profile that has Deadly Combat in it to load game for your older character, then use another profile that has Ultimate Combat to load the game for your new character. I believe you can do that with Wyre Bash, not 100% sure, but I'm sure someone will respond if that's possible with Wyre Bash or not.

Look for the Mod Manager for Skyrim, it lets you have a couple of mod mixes.

See this thread

http://www.gamesas.com/topic/1486166-2-simultaneous-installs-of-skyrim-1-computer/

And, read this thread about scripty mods and what to do with them, wade past the NMM and Steam Workshop posts to get to the good stuff:

http://www.gamesas.com/topic/1485056-since-i-got-this-on-steam-whats-better-nexus-mods-or-the/

Bash will let you have different profiles with different loadouts.

But AFAIK, it does not uninstall or remove mods from the game directory, it just disables them.

For a "clean" swap, you'll need to use something like MO.

The worst thing is that your character becomes unplayable due to CTDs and bizarre bugs.

The general rule is: don't remove mods from a current character and expect to have a playable game. This is especially true for mods with scripts. Skyrim stores references to those scripts permanently in your saves, and will continue to try to access those scripts after they've been removed.

You might be able to continue with that character for 20 or 30 more hours, but they will eventually become unplayable. That's from both personal experience, and a lot of posts over the last couple of years.

I haven't used it (yet), but http://www.nexusmods.com/skyrim/mods/1334/? seems to be the favorite for people who want to have multiple characters with different sets of mods. Wrye Bash is great for mod management, but probably a little harder to use and maybe not as good for different installations used at the same time (though it does support this).

To manually remove a mod, you should open up the original package (with 7zip), find every file it adds, and delete each corresponding one from the Skyrim Data directory. This is very important for any scripts it adds, especially the ones that override vanilla scripts.

You have leeway with certain types of files like textures or meshes, but scripts and animations at least should be carefully removed.

Another option is to either reinstall Skyrim and reinstall your mods with the Mod Organizer or Wrye Bash, or to delete every directory under the Data Directory, and reinstall all your mods, again using either MO or WB. I say this because MO & WB will track every file's relation to every mod, so you get 1-click installs and uninstalls, and even options to configure which mods override others, when there are file conflicts.

Removing a mod that uses scripts will only cause problems for a save if you play that save with the mod removed. So long as you don't play the in progress save without first reinstalling / re-enabling the mod in question nothing will happen to that character or save.

You could in theory have one character with Deadly Combat and another with Ultimate Combat and they would both be fine. If you were very careful about making sure to have the right mods when you wanted to play each one. Depending on the mods you might have to rebuild bashed/merged/skyproc/whatever patches each time too. That's where MO shines. You can use profiles to isolate the mods and saves from each other so you won't be able to accidentally mess it up and don't have to worry about the mods' files conflicting.

Thanks for the answers. Mod Organizer seems interesting but also like overdoing it a bit as we only are talking about a single mod differing between the setups. I think I'll take my chances - the only thing left to do for my ongoing char is basically to marry Vilja, as I'd like to try it at least one time (it's not really fitting from a RP perspective as they are best buddies more than lovers, but I'd like to check out how it's set up).

What I meant with my first question was if it helps to retain the scripts but remove the esp? That way the save would still find the scripts - but the mod wouldn't do anything.