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<steamdrive>:\Program Files (x86)\Steam\steamapps\workshop\content\244850\
Or something similar. If you are using local "offline" mods then they are still in your appdata folder.
Server setup is different than Single player/Clientside.
On my server box I noticed mods and saves were moved to ProgramData which is in the root of the server PC. So C/ProgramData
<steamdrive>:\Program Files (x86)\Steam\steamapps\workshop\content\244850\
A Dev told us so live on Discord = Don't mess in there ^^
edit
It is Steam that uses this folder and not the Devs.
After deleting the content of the Mods folder = they will all be REdownloaded but you must load them from a world save so they will be downloaded again.
Tho I can see those 700 Mods dowloading for verification in the game log file so they must be all redownloaded at some point.
C:\Users\USER NAME\AppData\Roaming\SpaceEngineersDedicated\Mods
= You are the best to know.
I've used the Portal search tool for Mod reports = 39 results
https://support.keenswh.com/spaceengineers/general/search/mod
Most likely because they keep the old data.
After this patch I had issues loading mods and blueprints from the workshop.
To fix this I basicly had to reinstall, but also making sure to delete the appdata files, appworkshop and appmanifest files (in the steam library folder) for space engineers.
After space engineers installed, it immedately downloaded (without launching the game) all my subscribed mods and blueprints to the steamapps\workshop\content\244850 folder. There is nothing in the appdata mod folder now.
Ok, I will send a report to the Devs about this and ask to have more infos about how to use this new "Mod system".
edit
I still have +700 Mods in the SE appdata.
Context? (because you said that already)
Are you saying you deleted spaceengineers and deleted the \SteamLibrary\steamapps\appworkshop_244850.acf and \SteamLibrary\steamapps\workshopappmanifest_244850.acf
and deleted your mod folder.
^This is all what I did.
Then once you installed space engineers all your mods went to your appdata folder?
If thats true, then I have no idea. All mine is in the workshop folder, it works though.
Also, for my dedicated server the mods for that gets loaded
ProgramData\SpaceEngineersDedicated\SpaceEngineer Server\content\244850
The dedicated server I also had to reinstall for mod loading issues
reported directly to the Devs.
https://support.keenswh.com/spaceengineers/general/topic/1-188-023-dedicated-server-dont-saves-modcrashes-slient-when-placing-modded-items
I posted a while ago that mods and save files were in a new location. Anyone with a whole new server install may find that the folders have been moved. I do not know the why or if it is Steam or Keen that caused it. Only that it is how my server is set up since the MP update Really does not matter as it all does in fact work.
Using their launch you have to sign into your Steam client account then you can just download any mods for your server that you are subscribed to as well. The one at a time adding mods is hard on the brain.
If you need more help feel free to ask in a steam chat. Add me as a friend. I have a dedicated server box and I run many games on it including this one. Be happy to help based on my own experiences and knowledge.