I'm trying to make the flying charm uncraftable with kubejs, but the crafting recipes for all charms are removed too.

Can't help without seeing your script

ServerEvents.recipes(event => {
    [
     Item.of('minecraft:potion', '{Potion:"apotheosis:extra_long_flying"}').strongNBT(),
    ].forEach((ingredientID) => event.remove({input: ingredientID}));
})

ServerEvents.recipes(event => {
    [
     Item.of('minecraft:potion', '{Potion:"apotheosis:extra_long_flying"}')
    ].forEach((ingredientID) => event.remove({input: ingredientID}));
})

ServerEvents.recipes(event => {
    event.remove({ input: 'minecraft:potion', '{Potion:"apotheosis:extra_long_flying"}' })
})

Same result for all variants, all charms are uncraftable. And not only charms, everything in the modpack that uses potions in the recipe, it's about 60~ items

Charm crafting is controlled by a single dynamic recipe; removing it will remove charm crafting entirely, and it does not have a blacklist.

Whatever issue you are seeing that removes everything using potions is just a result of the script being bad, but the functionality you want to accomplish is impossible.

@Shadows-of-Fire you could add a mobeffect blacklist tag and check it when you're also checking .isInstantenous()