I loaded Skyrim this morning on my laptop, getting ready to play. The first thing I noticed was that SKSE (and hence SkyUI) didn't seem to be running. No big deal, I thought. Maybe there was a patch and something will be updated. Then I got into the game, and realized that a couple hours worth of saved game had disapearred. Not a whole character or anything, but it took me back a level (from 22 to 21) and in what I lost I had completed several quests. Has this happened to anyone before? I don't know if this might have made a difference, but I just downloaded Dragonborn yesterday evening and hadn't played it since until this morning.
Is there any way to get that save back? If not, can I keep it from happening again?
It sounds like installing Dragonborn might have misplaced some files. I recommend reinstalling SKSE (and update to the latest version). I also recommend you go back through any other mods you're using and make sure you download the Dragonborn versions of these, should they exist. You may have some incompatibility problems otherwise.
Furthermore, did you go to your save folder and check to see if the saves were actually there?