Using this script to add rotten flesh as a compostable: js onEvent('recipes.compostables', event => { event.add('minecraft:rotten_flesh', 1.0) })
It works perfectly.
However, remove the script and then /reload again and it will still work. You either need to restart the game or use event.remove('minecraft:rotten_flesh') to remove it, despite the add script no longer existing.
This affects remove and removeAll too, their effects are not reset until you do a full server restart.

Versions (woops, forgot these):
Minecraft: 1.16.5
Forge: 36.2.20
KubeJS: kubejs-forge-1605.3.19-build.229
Architectury: architectury-1.26.40
Rhino: rhino-forge-1605.1.5-build.75

I am not aware of any mods in my test instance that mess with composters (its a light test pack of ~30 mods)