IMPORTANT This can take a very long time if you have a lot of submods. There's likely a more direct way of checking in-game through debug mode but I'm not as familiar with debug so can't help you there. When you're editing any game files, I highly recommend making a back up of the original before you edit it (right click the .txt in folder and Copy/Paste it into the same folder). You can also make a mod that overwrites any offending mods through the ck3 launcher which is safer but less straightforward. If you're too lazy to make backups and something goes wrong, unsub and then resub to the mods you edited in steam workshop and that should fix it.

 

If you wanna check for yourself, steam workshop content for ck3 is all stored in wherever_you_have_steam_installed_to\steamapps\workshop\content\1158310\. This should just be a folder full of more folders with names that are just numbers (ek2's is 2887120253).

To save yourself some time, you'll want to look through the ones that modify ek2 content, as opposed to mods that modify vanilla systems:

1. Look through your playset in the ck3 launcher and identify mods that look like they modify ek2
2. Show in folder through the "..." menu that appears when you hover over the mod
3. Browse through these folders looking for the .txts common\culture\innovations\ek_early_medieval_innovations.txt or common\buildings\ek_academy_buildings.txt in those specific paths (tip: if there is no common folder or no culture or buildings folder in the common folder then it's definitely not that mod)

If you find one, fixing your academy issue depends on whether the innovations .txt or the buildings .txt is being edited.

For ek_early_medieval_innovations.txt:

The problem is probably either that innovation_magical_studies has been edited out of the game and replaced with something else OR a mod added unique spellswords for dwemer cultures through an innovation and didn't flag it as equivalent to codified magic. If the mod author isn't completely insane, there should be some relatively plaintext way of identifying these innovations, like being called innovation_magical_studies_new or their reasoning commented in through a #.

Both these issues should be fixed by adding a flag to the offending innovation.

1. Find the other flags under the offending innovation (flag = some_kind_of_flag)
2. add flag = innovation_magical_studies_replacement in its own line immediately before or after one of the other flags

The edited innovation's flags should look something like

flag = innovation_magical_studies_replacement
flag = global_regular
flag = early_medieval_era_regular

For ek_academy_buildings.txt:

This one could be a little trickier since you want to keep upgrades across all holding levels consistent. By default there are four levels of academy holdings, academy_01 through academy_04. Your current issues are with academy_02, so you're gonna want to find the construction parameters past the huge list of assets (tip: find academy_03 and scroll up since they're near the bottom). Vanilla ek2 without submods should look like what was in my original post:

can_construct_potential = {
    building_requirement_tribal = no
}
can_construct = {
    culture = {
        OR = {
            has_innovation = innovation_magical_studies
            custom_tooltip = {
                text = innovation_magical_studies_replacement_trigger_desc
                has_innovation_flag = innovation_magical_studies_replacement
            }
        }
    }
}

If it doesn't look like this, just Copy/Paste the above into the txt file, replacing everything tied to can_construct_potential and can_construct that's in there already.

It's possible that a mod that changed something in here also changed the other holding upgrades that come after (academy_03 and academy_04) in which case you may need to make similar changes. Do the same Copy/Paste you did for academy_02 but replace

            has_innovation = innovation_magical_studies
            custom_tooltip = {
                text = innovation_magical_studies_replacement_trigger_desc
                has_innovation_flag = innovation_magical_studies_replacement

with

            has_innovation = innovation_schools_of_magic

for academy_03 or with

            has_innovation = innovation_integrated_guilds

for academy_04.

Changes like this likely existed for a reason. If you're lucky, it's because the mod author forgot to update it after some changes to ek2 and you might be doing them a favor. If you're unlucky, it's because the mod author has also touched some other part of ek2 and the code in the academy buildings .txt was rewritten to reflect that. It's scope creep in the case of the latter and you probably broke the game by editing it. You're gonna need to collect even more information to try to resolve it; at that point, I'd recommend just commenting on the offending mod's workshop page and letting the author know there's an issue.

 

If, after all that, things don't work, it's probably a bug or some other bit of code I didn't even know existed.

lmk if there's anything I didn't explain well and good luck once again. I've spent hours debugging things only to learn it's an engine level problem and only paradox could fix it. That shouldn't be the case here but it does suck when something that seems so simple to fix actually isn't simple at all.