That is an interesting idea. Sometimes cities are not connected to other cities. For example, in an early game, you may have copper, but one city is not connected yet. You can build axemen in some cities but not others. If the unit is built, presumably in a city with the resource, you lose one of the resources. Some of the cities may no longer have access to the resource. But, which ones? When the unit is destroyed, which cities should regain access to the resource?
There are several modcomps which attempt to implement "limited resources" similar to this. Most of these other modcomps put a cap on the number of units you can have; so if you have three copper resources, you can have three axemen. But you could not build a fourth one, and if you lose one copper resource one random axeman is destroyed. This avoids the problem of actually removing the resource. Would that mechanic work for you?