So....

[Martok]

I've never noticed any "unrest" issues when retraining the ruler's unit, as long as the province involved is well-connected to the rest of the realm. Obviously, don't send the King for retraining to islands subject to naval blockade...
And I wouldn't put him anywhere deep in the retraining queue in a frontier province - top spot or not at all. Wouldn't want to lose him forever if an enemy invasion was successful.

Agreed; couldn't have said it better.

One "gotcha" that annoys the heck out of me - if you upgrade the armor, morale, and/or weapons of your senior heir - and those upgrades aren't present in your most-developed province - when he ascends to the throne the upgrades will all be lost. Arrrggg! What, does he have to turn in all his up-to-date goodies for the traditional dynastic accoutrements?

Yep; exactly.

To be honest, though, I'd never noticed that. But then I don't upgrade my RK's that often, unless I already need to retrain them to replenish their losses. Royal Knights generally do well enough for me that I don't feel the need to upgrade them unless they're already right there in a province that has better weapons, armour, etc. Otherwise I don't bother.