Actually it works, with minor exceptions like ladders in maps from beta 1.
Just pack all the 3rd-party models and textures into the bsp (Packrat) under the original mod version.
Open the file with an entity viewer like EntEd and edit all the weapon ammo & armor entities to match the new ones.
The hardest part is to put the right weapon/ammo slot number at the right entity.
Having a decompiled version of the map where you can check which entity is placed on which location will also help.
Another way, maybe the best one, would be to edit the decompiled file in Hammer under B3 setup, make your changes on the entities, backup the file you will use in Beta3 and run a entity only compile.
The rest is copy & past of ammo, armor, weapon & player entities from the updated version to the other one.
You're asking: why doing this last step and not just using the entity compile version?
Well, try it and you'll discover why.