I have a mod that creates an enchant that goes from level 1-3, and having apotheosis enabled alongside it makes the enchant only go to level 1

What do you mean goes from level 1-3, is the max level 1 or 3?

Apotheosis does not reduce the default max levels of any enchantments, unless for some reason your default enchanting power functions were really screwed up (to the point where only level 1 was ever available in an enchanting table).

Could you show the source code of your enchantment?

The enchantment was made using MCreator, so it should have default code, but i'll send anyways. And it goes from level 1 to 3. It may also be a problem with Apotheosis AND Ensorcellation, so I'll test that. The actual function of the enchantment doesn't matter, since it's handled by a separate procedure, and still works fine. The way the enchantment procedure works is by doing a bunch of checks if you actually have it, are in the air, and have not air jumped more times than the enchant level, then overrides your motion vector, adds one to your jumps count and then does some funky particle/sound stuff, if you're interested.

(After enabling only my mod and Apotheosis:) The issue is with Apotheosis, not Apo + Ensorcellation. Checking only mine + Placebo fixes the issue.

Reset your apotheosis configs, then install your mod - if the issue persists, please pull your config file. The behavior you're experiencing shouldn't be happening by default, unless you booted the game with your enchantment and the max level got locked to 1 in the config.

I checked the config for my enchant. Found it, and found the culprit. I'm not entirely sure why but the max level was 1, but it says it was originally 3.

This is likely due to the fact it only went to 1 in my 1.0 build, but went to 3 in my 1.1 build. Not the fault of Apotheosis, but something maybe worth looking into a check/easy fix for. Perhaps having the default as a separate value that always updates to the mod's default, then having a changeable value and resetting that one if it hasn't been tampered with? Unneccesary, but would fix a small oversight.

This is likely due to the fact it only went to 1 in my 1.0 build

Correct - the config will "lock-in" a value at creation time and isn't retroactively updated, so if you booted with a max level of 1, it was locked to that value.