Compiling/model issues

I’ve extracted some models from a gmod .mdl files (npcs, they work flawlessly in-game).
I did this so I could recompile them with player animation (Nextbots eh) and generic male npc animations (the models use the normal valve biped).

However, the new recompiled model works flawlessly anmationwise, but I seem to have broken the collision somehow? The normal hitboxes are still there but the ‘bounding’ one is missing in-game. The npc behaves as it would normally, but I’m unable to hit it with a weapon (The area damage of an explosive does hit it the explosion is close enough).
The ragdolls after the npc has died because uncollide-able for a few seconds after every shot you fire into the ragdoll (it moves, then becomes uncollide-able for a bit, after which I can shoot it again, repeat).

I’m just completely lost as to why this is happening.

I decompiled and recompiled using Crowbar, perhaps there’s a better tool for this?
Thanks for any help