It's happened to me in the past with Syndicate too, so I can symptahise.
Firstly, the fact that WB is taking much longer to load than normal isn't too much to worry about. If your Amiga detects a validation error on the hard disk, it will attempt to repair the damage itself so the best thing to do is boot your system and don't go near it until the drive light extinguishes.
Once this procedure has taken place you'll be in a better position to assess the damage to your drive.
Do you have more than one HDD?
