If a capital ship or titan has more than one ship item artifact installed only one of them can be found in the wreckage after destroying the ship or titan and the other ones are just lost. I couldn't find them on any other ship or titan afterwards (surrendered and looked through all planets and fleets manually after another hour of playing to be sure the ai had time to reassign them if they still had them to another ship/titan) so i assume that they are completely lost for that save file.