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stilgarpl

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I was over my vassal limit, so to reduce it I gave many viceroyalties to single rulers. On their deaths, some of the duchies in those viceroyal kingdoms became independent of my empire.
 
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rageair

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Do you have any additional info? Were you under your vassal limit after you had transferred the viceroy dukes? Were the viceroy kingdoms over their vassal limit? Do you perhaps a savegame before/after/both where this is present?
 

stilgarpl

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I think I know what's the cause is: I am near my limit (42/43) when my viceroy dies, and his vassal counties and duchies transfer to me. This makes me go over limit - and then those events that make vassal independent ("True and loyal vassal" and "We are not pleased" ones) on inheritance fire and they go independent.

That viceroy might have been over limit too, because I gave him 6 large kingdoms (Poland, Pannonia, Germany, Pomerania, Bavaria and Great Moravia)

This is ironman, so I don't have a save before it happened.