I am a bit lost. Do we still need the mod fixer with patch 2 or not ? Only for some mods ? But can make others mods crash?
You should not need Mod Fixer.
Make sure all your mods have been updated for Patch 2. Or at least get confirmation that they do not need updating.
Remove Mod Fixer and if your save loads then you do not need Mod Fixer. If your save does not load then you do need Mod Fixer.
Without Mod Fixer you may get a message (something about a data mismatch IIRC) but this can be ignored. If you use ImprovedUI that will remove the message.