For every install in a multi theater setup, each should also have its own exclusive mdlnames.txt, callsign.dat and descript.dat. In the mdlnames and descript files, you should have the names of every addon inf object, weapon and ship, following the same formats as already present in these files for existing items. The callsign file should also have the callsign names and sim coding of every ship addon, each in its proper classification.
Following these procedures religiously with every addon inf object, weapon and ship will go a long way to preventing this error message in FF and QC. This also has its benefits in MB loading. Whenever the sim is loading any of these three (FF, QC or MB), it cross-checks the entries in the mdlnames, descript and callsign files with the contents of the AIRCRAFT, SHIPS, SCENEDB\WEAPONS, SCENEDB\INF, SCENEDB\VEH and OBJECT_DP folders. With the exception of addon aircraft, everything else has to be properly represented in the mdlnames.txt, callsign.dat and descript.dat, just like in the beginning when your sim was box stock.