When you upgrade from one version of Fabric Manager to another, there is a way to prevent the loss of map settings (enclosure names, placement on the map, etc.)
The $HOME/.cisco_mds9000/db directory contains all discovered fabrics (*.dat) and maps (*.map). These are upgradable between 1.1 and 1.2. If you need to clear the fabric cache, you should first export the enclosures to a file to avoid losing them. Everything else aside from enclosures and map coordinates are stored on the switch. The preferences, last opened, and site_ouis.txt format doesn't change from release to release.