Pain this one – but thanks to help from the foswiki IRC channel an answer was found.
Originally our wiki was a TWiki wiki. This was then converted to a foswiki – check into the story of the fork to see why.
Yesterday I ran a Debian style apt-get dist-upgrade which upgraded the foswiki package. This then meant that when looking at a web on the wiki I could not see that left menu and instead was getting ‘Warning: Can’t find topic .WebLeftBarWebsList’.
The reason is that the calling page is actually looking for ‘TWiki.WebLeftBarWebsList’ where it should be looking for ‘System.WebLeftBarWebsList’. This is a hangover from the conversion from Twiki to foswiki.
The answer is relatively simple. Go to the main web and in the middle of the page click on Main.SitePreferences. Then at the bottom of that page add the line ‘ * Set TWIKIWEB = System’ (with the three spaces at the beginning). This then sets a variable and the left menu bar should be visible when you are in a web.
Much thanks goes to gac410 on the foswiki IRC channel for fixing this for me!