Steam wants to do a "content conversion" of Skyrim's installed files. Since I have a working modded game, I'm leery of any process affecting Skyrim that I don't understand.

What will this content conversion do? Will my cleaned Update.esm need cleaning again? Will the conversion fail in some nasty way since I've modified Update.esm? Will mod files, or tools added to the exe folder like SKSE or Wrye Bash be affected? Or is it painless?

(I discovered Steam's intentions when I tried launching it through the regular Launcher to reset the ini files, but cancelled when the warning came up. It doesn't trigger when running it through the SKSE launcher.)

No.

And please use one of the many threads on the conversion already.

Edit for clarification:

I'm referring to the general question that is the thread's title, by the way. It will not interfere with things. You'll need to redo some things as per the next post, but it won't interfere in the slightest.

Yes, it will, along with any DLC masters you have too. The conversion forces a cache validation when it's done which then requires that Update.esm, Dawnguard.esm, and Hearthfire.esm be cleaned again.

Oops, sorry. A search for "conversion" turned up zero hits. Do you have a link to one of those threads?

That's reassuring. It sounds like restoring the original dirty versions from backup will help to avoid the extra download time.

Sure thing: http://www.gamesas.com/topic/1422033-game-content-conversion-link-to-image-what-is-this/

Alright then, lets use that one.