We used to have a script (courtesy of 1/4Life) to automatically refresh our spawnlists. However, a certain Garrysmod update stopped that from being possible.
So, whenever you update SBEP, I would recommend you update your spawnlists by going into the garrysmod/settings/spawnlist folder and deleting the contents. 
They will then be recached next time you start a game. This is especially worth doing at the moment, whilst I am updating lots of part names, making the 
old spawnlists redundant.

Also, you may find old dupes no longer work after recent updates, due to the model name changes. FishFace60 has written a script which can fix your dupes for
you. Just type SBEP_FixAllDupes into the console.