I seem to remember that they retconned a lot of the dumb quirky stuff and brought it back to a more reasonable tone. If I'm remembering right, they changed Dr. Clef's official story to that he's a boring elderly researcher who's never even seen a containment breach, all the over the top stuff was a prank some younger researches added to his files to get a rise out of him, and that his only response was to check with a superior that his original research was still intact before getting back to work.
I thought that was a pretty clever way to save face in light of realizing you were being a cringy autist. They also removed a lot of the weirder elements like turning dangerous SCPs into agents and stuff like that that and brought the feel more back to a dry surreal horror world.
I don't know anything about what goes on behind the scenes there, I've never really cared, I just know the site is great reading when you're trapped somewhere with nothing better to do. It can get repetitive, but it's usually worth slogging through the junk to get to the occasional gem or clever twist on an old idea.
Also if anyone hasn't, give SCP-093 a read.