Hello!
When I equip gear with mods to things like inventory size or hotbar size, spend xp on these things, and then unequip/re-equip the gear, the xp effects are removed (points are still spent, but the effects are gone). For example, https://mods.factorio.com/mod/Exoskeleton%20Mark%20II Exoskeleton 2 mod or the "More Armors Mod" group of mods: https://mods.factorio.com/mod/Better-Power-Armor-Grid have this problem. I'm not sure if it's the other mods being poorly written and overwriting effects, or this mod isn't saved in a way that, when things like inventory space is "recalculated" it is persistent. Either way, given that it happens with every mod I've tried, I figure I would bring it to your attention.