You may be thinking of Prince of Wolves by Dave Gross. It is a Pathfinder role-playing tie-in novel.
Summary from publisher:
For elven Pathfinder Varian Jeggare and his devil-blooded assistant Radovan, things are rarely as they seem. Yet not even the notorious crime-solving duo is prepared for what they find when a search for a missing Pathfinder takes them into the mist-shrouded mountains of gothic Ustalav. Beset on all sides by noble intrigue, mysterious locals, and the deadly creatures of the night, Varian and Radovan must use both sword and spell to track the strange rumors to their source and uncover a secret of unimaginable proportions. But it'll take more than merely solving the mystery to finish this job, for a shadowy figure has taken note of the pair's investigations, and is set on making sure neither man gets out of Ustalav alive...
I read it a while ago and do recall that the two get separated. Radovan definitely gets involved with a "gypsy"/werewolf group. Don't recall the bit about the scar or academy for Varian. Good news is, if this is it, there are a couple sequels.