The reason this happens is unknown but it has affected my entire mod. The issue seems to be that the slot item is not activated for reinforced units. It is still present within the squad.
I have made a fix but it is not ideal as it takes multiple steps as well as considering all units that use slot items. Because this requires units to die it will not work when the squad is split i.e. picking up a mortar. Some things may also not behave normally when picking up other slot items.
In this example I have Fallschirmjagers. They have 2 FG42 and 2 KAR98. The weapon upgrade gives the entire squad of 4 FG42. Normally without this fix all reinforced units will have KAR98.
EBPS
Clone and rename a weapon in ebps\gameplay\props\ it doesn't matter what it is.
actions_apply_ext>delay>make_dead delay is required or it will crash.
entity_blueprint_ext>is_visible_in_game: false
Slot_Item
Create or clone a new slot_item.
drop_item_entity: the clone you made earlier
drop_rate: 1 this ensures that the item_slot is removed on the death of a holding entity
is_entity_user: true I think this makes it so an entity drops the slot item instead of needing the entire squad to die
slot_size: 0
weapon>weapon whatever weapon you want the slot item to be. Ensure weapon values are correct.
Slot_Item
This is a dummy slot item that is used to display the slot item icon after the upgrade is purchased. This step isn't necessary for most cases but because fallschirms use 2 FG42 from the start there should be an icon to distinguish them between the upgraded squad.
drop_rate: 0
slot_size: 2
Upgrade
Mostly a dummy upgrade. Its only action is to give the dummy icon to the squad.
SBPS
squad_action_apply_ext>slot_item_add>FG42 slot item you made, only one.
squad_action_apply_ext>requirement_action*3: see pics. Ignore animator_set_action as its for debugging. You will have to create additional requirement actions depending on the number of max squad members and/or upgrade types.
squad_item_slot_ext>num_slots: 2
squad_upgrade_ext>upgrade>upgrades: Change to the upgrade you made
So in conclusion here's what happens:
On spawn fallschirm are giving 1 FG42 slot item. The second FG42 is given from the requirement_action since it detects there are 2 or more members but only 1 FG42.
When the fallschirms die and there are no free units to swap the slot item to it will drop the invisible FG42.
When reinforced back to 2 it will be given an additional FG42 slot item.
The upgrade allows for the 3rd and 4th members to receive slot items.
I'll continue to try and find the cause for this problem as the fix is neither flawless nor simple. Hopefully the mod isn't corrupted or something.