I just upgraded from 0.9.16 to 0.9.17 and then tried to create a new repository. I then got this message (see screenshot):
The document "Repositories" is in the trash.
I didn't know what to make of this obscure message and so I canceled it. I appeared a few times more. Then I had to restart my mac (not because of MacHg) and after starting MacHg again all my repository bookmarks were gone. Luckily I found the "Repository" file in the trash (now I knew what this was) and restored it.
My guess is that during the "upgrade process" you MacHg simply moves the MacHg folder to the trash without keeping the "Repositories" file. Please don't do something like this.