On the contrary, Dukes rule in the name of the ruler. Just as Lords rule in the name of their Duke and landed knights in the name of their Lord.
In the medieval mindset, at least if one is properly RPing, power doesn't come from below but rather from above. It is why the "Royal We" developed. The monarch IS the realm personified.
Methinks this be bologna at any time before 1500 AD. Medieval kings, AFAIK, did not often operate under a "L'etat, c'est moi" mentality. Hence why absolutism is, well, called absolutism, and clearly post-medieval.
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That aside– couldn't this be solved by requiring that the capital be a ducal center? Or make it so that the REST of the duchy secedes, but not the capital?
It does seem really weird to me that a capital lord could veto an impending secession by switching his ducal assignment. It doesn't seem like he should have that power. "Oh, looks like Duke Joe wants to secede– I think I'll just hop over to his duchy, to lock it down."
And, as noted earlier: that means you just change allegiances, then secede a few weeks later. Which isn't really even an SMA issue: seeking refuge with a rival realm then being reconstituted as an independent power hardly seems unusual. I seem to have some vague memory from a French History class of Burgundy once doing almost precisely such a thing... hmmm...