Hi @egwarhammer,
The Mods directory is not touched during the "Repair Game" or patching process. Thus the existence of the Mods directory will not interfere with the file updates Origin is performing, and so technically does not need to be removed.
BUT just because Origin will be able to successfully update/repair your files does not mean you don't have a conflict with Mods. So:
- For Patching: It is strongly recommended to make sure your Mods are compatible with the new version after patching, as they are very prone to breaking the game (in particular Game Mods and UI mods). Of course now the game now automatically disables mods after patching to encourage that people follow this practice.
- For Repairing: If you are repairing your game, it likely means you are having a problem. If you are running with Mods it is strongly encouraged that you disable all Mods to see if that is the source of your problem.
Hope that helps,
SGMS