This new update is not specifically targeted at mods, or is anything malicious on Volition’s part. The reason that some mods are breaking is simply because the modded asm files need to be updated with a new index taking the new patched files into account. Known mods that are affected by this are the mission replay, customize all vehicles, wardrobe color changer, delete reward vehicles, and clip editor. There may be more.
We’ll be working to get everything updated soon. In the meantime you can still play the game by removing all mods with the following extensions from your sr3 install folder: *.lua, *.xtbl, *.str2_pc, *.asm_pc."