everything works fine again. Normally sign the ClickOnce deployment with my comodo codesigning certificate, but the smart screen filter still throws a warnig. I've read somewhere that this could be stopped if you sign the assembly too.
I tried to sign the assembly with a new keypair (my certificate can't be used for that), and i think this was the reason why the references get lost while deployment.
Now i only sign the ClickOnce deployment and it works like a charme.