I have never seen that... Sounds like a bug.

In my English campaign I had a crack force of Spanish Grand Inquisitors (I didn't expect the Spanish inquisition)

Those guys burned their way through the Italians who were by this time getting a bit troublesome (they had Taken Constantinople and were living the high life in Greece and Asia Minor, their fleet was large and trying to sink and blockade my ships).

Anyway within a few years all of their Kings are burned as Heretics and their royal line comes crashing to an end, all their ships vanish.

When they Emerged again 15 years later in Greece (The Mongols took Constantinople and their other Asia Minor Holdings in that time) they didn't have a fleet and remained stranded there between the Hungarians and the Horde.