I managed to go to Blackwater and find the note on the corpse in the house and go to the Repositiry before getting the Amulet. I saved in the secret room at the inn and then when I realized going to the Repository meant death I reloaded and pulled the lever to get out. I then completed the appropriate main quests and tried to get back into the Repository through the inn but I can't register under the secret name again.

Is my game now broken? Is there any way for me to continue?

What version are you playing Book I with and where did you download it from?

Actually, never mind. My genius self just patched the game without backing up his saves. Ah well, wasn't entirely happy with my build anyway.

So where did you purchase Book I from?

Bittorrent. Originally purchased it from the Basilisk site a couple years ago. Went to play it again a few days ago and didn't know how to redownload so I torrented a copy. Why?

Because bittorrent, aside from being an illegal distribution, is not a trusted source. The person who put it up there may have altered the game in unknown ways. Normally, updating the program itself should not have any effect on the save files.

If you had wanted to download the latest version from Basilisk Games, then simply emailing info [at] basiliskgames.com with your original invoice--or even just from the email address that you used for the original purchase--would likely have given Thomas enough information to find your original order and activate a new download link for you.

Because the problem you described was solved in a patch that was available only a few days after Book I was released. I got the impression you had illegally downloaded Book I because all legitimate businesses selling the game should have the latest version and you confirmed this.

If you genuinely did purchase Book I a couple of years ago direct from Basilisk Games you should update to the latest version. Kreador Freeaxe has already told you how.

Thanks. I'll contact them about getting another download.