Repository problem.

So I did some cleaning in my mods folder and now when I started beam again the repository wants to download all the deleted mods again. Is there any way to stop that from happening apart from going to each mod individually in the painfully unresponsive UI and unsubscribing?
--- Post updated ---
POST UPDATE: I moved all mods elsewhere, went in game and told it to delete all my mods, then moved my mods back to the folder. I'm coming back to the old fashioned manual mod downloading I did for a couple of years before repo came to life.

 

Yes, done that, posted in the post update.

 

it won't delete manually installed mods, only repo mods, you have to manually delete manually installed mods through either the individual delete button on the mods in the mod manager, or by deleting the files

 

Maybe, although I was not gonna play a risky business with my monthly internet transfer worth of mods gathered through past few years. I'm fine now tho.