Updates remove all installed mods. You will have to reinstall them in the same order and with the same options. But even then, I think old saved games may break. So if you have an ongoing game, it's safer to finish it before updating.
General rule of thumb: Updates will always break mods, and reinstalling mods can break savegames/will cause weird glitches. If you are in the middle of a playthrough that you feel good about. FInish before updating. Then you can reapply all your mods for a fresh playthrough.
Considering you have another 60-100 hours of playtime left, I would just uninstall the game, and a new reinstall with the new patch. Then add your mods and do the dungeon again. You haven't really done that much in the game yet. At least that's my opinion.
Comments
Are there patch notes somewhere?
And thanks!
A BGEE/SoD/IWDEE updates are about to come, so if you're planning to play one of those it is wiser to wait a bit.
Thanks for the update, though!