Hello Madscientist,
I know what you mean. The same thing happened to me. My help file went to 0KB and the file chane date was 12/31/10 at `11:38 PM... Well I hadn't even used my laptop that day, and I was doing the New Year's thing with family...I read the bug posts and downloaded a new main.htm to replace mine. When I opened the help file in Synergy editor the links were broken, just like yours. Here is how if ixed it:
I am using Windows 7, and I am able to revert back to a previous file version. So, I replaced my broken main.htm with one saved from 12/9/10. Everything is working fine now. I assume the link issue is an adminstrator permissions issue thing, I guess... I don't know, but that fixed it for me.
-Snurg