Strange, I just tried it again with the L4D2 version of Hammer.
I export from HammUEr to my SteamLibrary\steamapps\common\Left 4 Dead 2\left4dead2\materials directory, which creates a HammUEr directory under it.
Then when I start the L4D2 tools and Hammer, It Just Works.
I can filter by hammuer in the browser, and the textures match their Unreal Engine originals.
Is there a mismatch between the directory you put them in and what the .vmt files reference? Because those include the HammUEr\ prefix, so if you changed the directory name, you might need to edit the .vmt files as well.
Thanks for the reply, but it turned out the problem was my fault. I didn't realise the materials I was trying to export used textures that didn't comply with Source's resolution requirements (they weren't powers of 2). I just had to resize the textures and now everything works fine. On a side note, the manual states that thumbnails in Hammer's texture browser don't work, but they actually do work just fine. The only issue I've noticed so far while working with the tool is that textures on really thin faces (2 units wide or so) get a little broken when imported to UE - part of the texture seems to disappear, leaving a small "gap" near the edge of the face.