The configurations for your workspace are saved in the workspace's .metadata/plugins folders. This should include all your configurations for servers, drivers, profiles, etc.
If you install JBDS 11.x and select your 10.x workspace it should warn you that the versions are different, but your work should be preserved.
Note that a new install of JBDS is required because moving from 10.x to 11.x changes Eclipse minor versions. Eclipse does not provide the means to upgrade, just install new instance.