That's not the problem. Here, open this map:
Once you scale a brush and build the map it fucks everything up. You have to start fresh, you can't even have the old map open and rebuild parts of it. I'll bet you can reproduce the error by importing your map into this and rebuilding the whole thing.
Pitchfork mob stands ready. Let me know when I can send them over
I kid you Funky, this is how we all get better. I know this sucks to find out. I hate it too since scaling brushes is such an easy way to fit things. You just can't use it with subtractive geometry because it destroys the BSP calculations.
EDIT: I tested and it did exactly what I thought: When you copy my map over into yours my new area behaves like yours does. Inventory is deleted. The lava zone is leaking out all over the map because the BSP tree is corrupt.
This is two room separated by a simple zone portal. Lava zone identical to yours is in the other room. The result? No weapon loss. You can even directly swap your lava zone into it and see it still won't have the effect.