Ok, here's what I think happened:
1) you upgraded FMP, which had the corrected id field
2) you loaded your savegame, got the warning, and saw that FMP items had disappeared -- this was because the updated FMP had a different id, and was disabled by default in the mods screen
if you enable the new FMP version in the mods screen and load your save, you'll still get the warning (since the mod id has changed), but if you allow the game to load, all the FMP items should be there now.