As far as I can tell, this issue was related to the web.config pointing at a 32 bit hg.exe that did not exist. This is a 64 bit server.
Once I fixed the line the web.config, the upgrade was successful and things look OK again.
The error was:
<add key="hglab.general.hg-executable-path" value="C:\Program Files (x86)\TortoiseHg\hg.exe"/>
The fixed line is:
<add key="hglab.general.hg-executable-path" value="C:\Program Files\TortoiseHg\hg.exe"/>
I had noticed during the upgrade that I had to change the path of the hg.exe.
I think this might be common when I upgrade HgLab but it's been awhile so I can't remember.