I haven't tried using Crowbar to actually decompile the custom skins for L4D2, but the last endeavor I put into decompiling a custom L4D2 model with regular old MDLDecompiler successfully, the actual reference .SMD file was completely empty, and I found out after asking over on Facepunch that it wasn't possible to decompile a custom L4D2 skin and retain the model (at least at the time). I can try taking a quick look at seeing whether Crowbar is capable of it or not and save you the effort of finding out, so I'll grab a random skin and take a look.
I'll update this post with the results.
Edit: 8 minutes after this post was made, I managed to find a skin worth testing this out on, and I can confirm that Crowbar will successfully decompile the model and leave the reference file in-tact (meaning that the model is definitely included upon decompiling a custom model). Just download the latest version of Crowbar, and you should be good to go.