Ok so I was getting "NHibernate.MappingException: Unknown entity class" for a revised/renamed class in my project. "Aha!", I thought, "its not an embedded resource!".. and it wasn't. Re run my tests to confirm update worked... neagtive.
After about 30mins of seraching I noticed I had clipped the name too much and had removed the .hmb. part out of the file name in the mapping file... well thats annoying!