I've seen various people complain that upon upgrading their BOINC version, their old work would no longer be around. This seems to be a problem when upgrading from a 32bit BOINC to a 64bit BOINC, where the data directory is left behind. But it mostly happens for people who inadvertently install the wrong BOINC, where they have 64bit and install the 32bit version.
Perhaps something to do with the different c:\program files\ and c:\program files_x86\ directories, so the old BOINC isn't uninstalled but rather deprecated?
The latest report I saw on this was by BeemerBiker on the BOINC Dev forums.