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.

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?