I recently converted a finished CK2+ game, in the hope of continuing into EU4, but even though the HRE was very fractured and decentralised, the emperor still got a lot of land, even though his personal demesne wasn't more than the de-jure duchy of luxemburg. To elaborate, the HRE consists of the areas of france, normal HRE, Italy, de-jure Jerusalem and some random titbits in the mediterranian and other parts of the world. As said previously, the emperor only owns de-jure Luxemburg, and the rest is allocated to dukes who all own most/all of their de-jure lands. Very few kings (Bohemia, Sicily, Jerusalem), mostly dukes with a few large counts (of provinces that carry over to EU4, like Nassau or Nürnberg). Crown law was only low. Even because of all these measures in place, the emperor has lands ranging from half of southern italy (in CK2 fully owned by King of Sicily), to northern Pomerania and Danzig (owned partially by me as Margrave of Brandenburg and partially by my family member the duke of Pomerania), even parts of southern france, which were owned by the duke of Gascony and the duke of Toulouse. Both dukes do exist, but only as OPMs, not as countries that have the land they need.
I am using the v4.06 Beta 5 (the one claiming to be able to work with the newest version of CK2), as well as 1.20(Ming) in EU4. I did use some minor mods in CK2 (more retinue from buildings, as well as a new CB), but none that changed anything important. In EU4 I used some mods that also change nothing to the map, so there shouldn't be the problem. Any ideas/tips on how to solve it?