The scenes and voices and such work because they're stored outside of the maps. Extracting the first lump from each bsp that replaces an existing file should fix this.

That error occurs because the lump no longer matches the map.

Most HL2 maps have the entity lump outside the map, because they were patched at some point. Newer versions of the engine can load lumps from sources outside of the map files. It's caused by a newer engine feature that they make use of. The error at 2:07 isn't related to the engine version.