https://pastebin.com/MQ1pdUqR

No issues with the overworld or end, only the miniboss "wither_Archer" in the nether.

Do you have any Apotheosis addons installed? Or have any apotheosis related datapacks loaded in game?

I have now tried to remove the addons, but the same problem shows up. No datapacks at all!

I am not able to reproduce this issue. Withering archers under normal conditions are able to spawn as expected. Apoth provides three unique gear sets for the #the_nether_bow tag - https://github.com/Shadows-of-Fire/Apotheosis/tree/1.20/src/main/resources/data/apotheosis/gear_sets/the_nether

You can use a datapack to override that specific miniboss with the false condition, which will remove it.

I don't have any experience with making datapacks. Do you have a link or guide to disable that miniboss? or perhaps a way to disable the spawns in the nether specifically? I really enjoy the mod, and would hate to remove it :c

You can base off of this export of the base apotheosis data files from 7.4.0
stock_1.20.1_7.4.0.zip

You would then erase every data file you don't care about (those in data/), leaving only the withering archer file (data/apotheosis/minibosses/the_nether/withering_archer.json)

Then replace the contents of the withering archer with the false-condition:

{
    "conditions": [
        { "type": "forge:false" }
    ]
}

You will then have a datapack that, when loaded, will disable the withering archer, which should resolve your issue.