You have to click on a storage unit while it's equipped to toggle/activate LOAD mode so that it can take matter with it when you put it in your inventory.
The only way to transfer matter from one unit to another would be to have them both attached at the same time and set the larger one to LOAD, then detach it. Then you'll lose nothing except the attach cost of the second/larger unit.
Shouldn't the matter it contained drop to the floor on unequip? You could label the storage unit's modes: Load and Dump (the latter would be the current unlabeled mode but with matter dropping to the floor). That would also allow a more intuitive way to swap matter between units, even if it would take more time. To me at least, the matter disappearing into thin air reads like a bug, and can be frustrating if you just walked around filling a unit to fabricate something (especially if it is a Hcp. unit).
EDIT: in case there is any confusion about the behavior here: If you have (for instance) a small m. storage unit which you have filled to 50 while carrying in your inventory, and your core matter stores are currently full, if you equip the unit and then unequip it without setting it to Load, the 50 matter just get eaten by the game.
I suggest giving the matter storage units three modes:
- Load: Same as now: attempts to completely fill the container from your total matter stores when unequipping.
- Overflow/Storage: Only takes with it whatever overflow exists due to its removal from the core, if any (if none, it remains empty). It might be simplest and most intuitive to make this the unlabeled default state.
- Dump: Like the current unlabeled default state, except the excess matter is dropped to the ground rather than destroyed.
Anyway, I'm not trying to drill anything into the ground if that's how it seems - let me know if I've gone overboard trying to clarify.