Current settings are saved in ctrlsurface.dat (in user hidden folder, use Search to find it). In case it is corrupted or lost, SONAR rebuild it with empty configuration. Most probably your case. But the same can happened in case you have started SONAR as a different user (check your Windows login settings).
If you save plug-in settings as preset, it is saved under "Shared Presets" folder ( also user hidden folder) and the file name is the preset name (so you can search it directly).
In case plug-ins are lost/corrupted/unregistered, the configuration should still be there. But surfaces will be unusable.
*.chm are help files, plug-ins are *.dll (the name part is the same).