All the settings (rules etc.) are stored in this folder: %AppData%\MAD. You can open this folder in explorer (open explorer and just copy paste that location into the address bar and click enter). All the files inside this is what describes the settings that the program uses including global filters.
If you have lost rules, then this means that this folder is either corrupted or the contents were cleared/deleted. This can happen if you ran certain cleanup tools or have processes that cleans up filters.
There is also a folder %AppData%\MAD_BACKUP that stores backup of settings in the format of .MDZ files BY DATE and version of the program. If you want to restore an older setting you can use the Export/Import tab to first Export your CURRENT settings to a .MDZ file (save it on the desktop) and then IMPORT one of the older .MDZ files in this location. This will restore older configuration.