On the other hand, I can see how it could become a logistical nightmare to ship the new and improved (swords, shields, various armor pieces) Also, trakcing every individual unit and the huge variety of gear (instead of tracking an army that has 3000 "swordsmen" the program would have to track each unit as an individual with his own unique gear, etc etc) That sucks too.
Well, one way to solve the problem of having to track every individual unit is to train squads of units, each of which is identical and thus significantly reducing the problem. Each of these units would still have their own identification number or whatever, but to find out equipment information it could just point to the squad-wide information. Splitting a squad would be like creating a new squad.
This would be so that all swordsmen units in the world are the same.
This is one thing I want to avoid. In almost every game I've ever played, once you research higher tech, the older becomes totally obsolete, and it gets old. It'd be awesome to have the option to produce lesser quality equipment even once you can make higher quality stuff. Its advantages would be higher production rate, lower production costs and lower maintenance costs. This would add a great deal of depth, I think, at a reasonable cost of complexity. I'd prefer if this were true regarding all equipment, but as long as it's the case regarding special vs. standard weapons (ie, "Flaming Swords of Death" vs. Swords+X) I'll be satisfied.
Now, onto the hard part... How to handle upgrading with such a system. I think the best way is to require uniting troops with their new equipment. This can be done by sending the troops to a city with a store of the equipment or the ability to produce it, or by sending the equipment to the troops. The latter could require the target forces to remain stationary while the equipment travels, or not - I don't know which would be best. Either way the logistics could be largely automated. When you click upgrade, and choose what to upgrade, a list of possible methods and their time requirements can pop up and the highlighted route displayed on the map (including both troop and caravan movement, if relevant). When you choose your preferred method, the computer will make what needs to happen happen. There could even be an option for your troops to return to their previous location when upgrading is complete.
In the case of actually retraining (or further training, if possible), troops should have to be sent to an appropriate settlement - but again, the computer should assist you in finding appropriate destinations and getting your troops there (and back).