After running a Joomla and VirtueMart update in place the admin menu dissappears, and this is a known issue. I found in our circumstance that the main menu item for that menu was missing.
The result was a Joomla whitescreen and on inspection in the browser console an error could be seen stating subquery returns more than one row.
All admin menu items can be seen using this query:
select * from `#__menu` where path like '%com-virtuemart%'
The way I was able to fix it was to simply delete the menu items using a query, and then do a select and insert from a working installation. As long as the component ID matches up (which we had as 10000) then it should work perfectly.
VirtueMart constructs the menu wtith addBackendMenuEntries in the updates_migration.php file so it is likely that there is a fundamental issue there.
