Some mods, like for example http://skyrim.nexusmods.com/downloads/file.php?id=9494, tell you to make a clean save before installing it. But attempting to create a clean save appears to corrupt my save instead, provoking many CTD's. Here are the steps I took:

1. Dismiss all followers and move to an interior cell.
2. Save my game by creating a new file and shutting the game down. (So no quicksave, autosave or overwrite).
3. Deactivate all mods, start up Skyrim and load my save.
4. Save the game again, and shut it down.
5. Activate all mods, including the new one, and start the game.

I have discovered that deactivating all my mods corrupts my save game, causing many crashes. One such a crash persistently happens when summoning Bound Swords.

So what is the safest method of creating a clean save?

I don't have an answer for you, but judging from some discussions I have been reading on the forums, it seems that the game stores different sorts of data in different sorts of ways on your save files than it did in Oblivion and Morrowind, which results in some presumed-to-be "safe methods" not working properly.

At least this is the impression that I got.

Shoud this be Oblivion, I would suggest you to skip the mod deactivating part. In some updating cases you could want to follow all steps BUT deactivating only the mod you are updating not the rest. In Skyrim case, considering the persistence of scripts, deactivating all your mods and then activating again is probably the worst thing you can do not counting things like deleting random files.

If you are updating Warzones, you may want to create blanck script files named as the ones in that mod, overwrite warzone scripts with the blank ones and follow all the steps BUT (again) only with pluggin files from Warzones (finally overwrite the blank scripts with the real ones).

Thanks for the replies.

@Amgepo: How do you create blank Script files?

With the CK. remove the script to uninstall Just place an object in the world (could be a quest or a dialog instead) go to the last tab, script, add one script, name it as the script you want to clean, rigth click, access source code. Build, compile, save (the script, not the esp). Now exit the editor without saving (you don't need the object, just the script.

Once you have a blank script, you can just rename it, istead of creating a new one.

IN Oblivion, updating and getting a clean save for any particular mod meant loading the game, creating a new save, exit and unload that one single mod. Load the game (will complain of missing content) and create another save. This new save is now clean (OF that particular mod) and you exit. Now install the update. load the game, Play as usual.

I would never do any steps more then this for any mod. I was loading FCOM with 200 mods and never did more then that to update any mod.

Of course this is now Skyrim but i fail to see how it would be any different.

Fallout 3 and Fallout NV were the same, when creating a clean save only disable the mod you are updating.

imo, if a mod required clean save, i suggest stay away from it.

sooner or later, you gonna runs up problem either with: next patch, or another mods, or the mod no longer be maintain.

That's an interesting point of view. To say the truth losing stability makes the game less enjoyable. To compensate that a mod should add really a lot of playability.

only few mods has this "disclaimer" put up that required clean save, afaik.

I played with many mods, and i explicitly avoided such mods. not that i said these mod is bad or what, it's just not worth the risk to have a dead-end problem, as the mod already highlighted the potential risk.

it's clear that the modder already has no confidence in his own changes.