The size of the model doesn't matter, if you still use the monster_gargantua entity. The size of the boundary box is defined by the entity itself.
However, VHE with model-rendering-support won't display the actual boundingbox anymore, so you'll have to either check the .fgd or find an old .fgd and replace the current one with it. Then if you got the real size, just put the latest .fgd back into the folder.
If the original sized gargantua will fit into your room, the resized one should ,too.
If that does not, you should upload the map to the propblems vault.