I have 3 golden rules related to Mods and Sims games, which has applied to all of the Sims games back to the original.
Rule #1: Do not load a game you played with mods after a game update until you have updated all mods that need updating (and gotten the all-clear from the mod-authors on the rest).
That means not playing that save for a while after the game first updates or, what I do, making sure your game doesn't apply the update until your mods are ready for it.
Rule #2: Backup your save games when the game gets an update, in case you think you followed Rule #1 but one of the mods still causes a big problem. (It's worth doing this regularly regardless).
Rule #3: Don't use mods if you aren't emotionally ready to lose an entire save. If you follow Rules 1 and Rules 2, you should be fine....but you know... ____ happens.
I have never used a mod that "resets" it's settings when updated. But one solution when that happens is to load the game, get all the settings set, then exit the game without saving it. Then reload back into the original game saved before the update.
Most mod's with advanced settings like that are saving them to an external file in the mods folders, so once you get them set they stay set. MCCC saves it's settings to a file named "mc_settings.cfg" in the same folder under /mods where it is located, for example. When updating MCCC, do NOT delete or replace this file and your settings are retained.
I suspect you may have lost your settings not because of the update, but because you deleted the file that held the settings when updating mods.
