Those Castri did not even exist before the Calamity though - there was only a single castra established in Eorzea in the Sixth Astral Era located in Mor Dhona (Castrum Novus), that was Nael van Darnus's base of operations. Castrum Novus was destroyed in the Calamity, being sited right next to Carteneau, and following that when Gaius and the XIVth seized land throughout Eorzea to build new castri he simply took over what was left of Castrum Novus and rebuilt it into a new castra, renaming it in the process (Castrum Centri).
It's highly likely the surviving VIIth troops, if any, were simply absorbed into the XIVth, but it's equally likely they all died at Carteneau, given their zealous devotion to Nael.