If you are going to mod a game first learn about modding that game.
'Stripping' out mods mid-game can and often does result in the game or saves refusing to load. Depends on the game and depends on the mod. The solution to this is not to do all sorts of irrelevant actions such as verifying files and the rest of your list.
Okay so you download Patch 2 and your saves refuse to load. Lesson 1 - correlation is not causation. Lesson 2 - here is what I would have done if I had downloaded Patch 2 (I run mods but I never download patches or anything until I am convinced it works).
I would try a new game with the Patch installed. If a new game wont have it then it could be the patch.
I'd first try removing the Mod Fixer mod in case Larian had made it redundant (as they tried to do with Patch 1). If the save wont load without Mod Fixer then it is the long road.
I would have removed the Patch 2 .pak file from the Data folder and tried the save.
I'd visit Nexus to see if any of the mods I use have been updated (I have tracking activated for the mods I use). Downloading any that have been updated.
At this point, depending on how long Patch 2 has been out, I might decide to wait a day or so to let more mods get updated.
If not I would uninstall one mod at a time (still without the Patch 2 pak file) a try loading the save. If the save loads then leave the mod uninstalled; if it doesn't load then re-install it.
Once I'd worked my way through the mods I would place the Patch 2 pak file back in Data and try the save (probably wont work but you never know).
If it doesn't work then remove the pak file again.
Now I would try installing any updated mods after first uninstalling the previous version. I'd do this one at a time checking whether the save loads.
If I end up with a save that only loads with some or all of my mods but not mods and patch then I have a decision to make.
