Before starting Skyrim this morning, Steam said it wanted to change the format of the Skyrim (not Steam) files to make them more efficient.

Has anyone let Steam do this yet? IF so, has it affected being able to use mods or start with SKSE, etc,?

It's okay, I have no problems at all.

There's a bit of information in this thread: http://www.gamesas.com/topic/1422033-game-content-conversion-link-to-image-what-is-this/