For patched VI I've just run a few tests. Upgrades for weapon, armor and morale are all additive, and all checked during retraining. Retrain a unit of gold weapon upgraded peasants somewhere you've got a cathedral (but no armorer/metalsmith), and you get unit of peasants with morale+3 and attack+4 (oddly though, the combat screen seems to suggest the morale+3 is actually morale +6...anybody know anything about this).
Unit damage isn't a concern. A unit of 48 armor +1 peasants retrained in a province with no armorer but a master metalsmith becomes a unit of 100 Weapon +4, armor +1 peasants.
Another thing to consider is build times. It's been stated that on huge size, units take 2 turns to build, but only 1 turn to retrain. However, expanding on that is a very simple principle - retraining always takes one turn. On normal sizes, Varangian Guard, Joms Vikings, and Berserkers all take 2 units to train, but only one to retrain. Training a unit of Varangian Guard on huge unit sizes takes a rather lengthy four years. Retraining a unit of Varangian guard, even if it's just one Guardsman, takes but a single year. To say the least, anyone playing Huge size with the Vikings has good reason to consider retraining.
I didn't get a chance to determine how valour upgrade buildings function, and though I seriously suspect they function on the level of the individual instead of the unit, I'll run some tests before I say anything for certain.
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