If I understood the zone functions correctly, and they haven't changed, once you take control of a base that is a part of a zone controlled by an enemy, it is no longer served by the resupply system, and would require supplies to be flown in by your country. I may be incorrect, but this is the way I believe it works (or at least worked this way in the past. Some maps seem to have only 1 zone, so this may no longer apply).
Also, if this hasn't changed as well, you can blow up either the engine or one of the first cars in the train, and the rest will sit there until the next resupply train leaves that depot. With regards to the truck convoys, there used to be some sort of variable in those as well. If the strat was at, say, 50%, the trucks would only provide half the rebuilding effect that they would if the strat was at 100%, with the lead trucks pretty much always having supplies, and the trailing trucks being the ones that are pretty much null when the strat is damaged. I'm really not current on any of this stuff, preferring to put ordnance on people, since strats don't whine.

I think that's all in the help files, but I can't say with any certainty whether or not this information is still accurate.