Aye, in Civ3 resources can be extremely volatile but will always maintain their starting balance (disappears one place, reappears another). The Next War scenario for Civ4 has net-negative depletion, but the whole premise is environmental collapse so it's a unique example.
This is precisely the type of mechanic that I think the game should avoid: "maintaining their starting balance" as a random event. You the Civ should have to actively Hunt for replacement deposits/resources, through map exploration, new technologies, trade, etc. And, unfortunately, there is no automatic 'maintaining the ... balance'. For a Worst Case example, look at the world-wide depletion of fishing stocks that has been going on for a couple of centuries but has accelerated disastrously in the last 50 years.
On the other hand, as an example, mineral resources could be subject to a distinct Technological Progress revealing New deposits:
Basic Mines (Neolithic to Medieval) allows shallow mines that can dig out deposits only near the surface, but would be sufficient for the small quantities required then - it only took about 100 tons of Iron to equip a Roman Legion of 5000 men with metal armor, weapons, helmets, etc.
Deep Mines (Medieval to Modern) - the advent of sophisticated timber frame reinforcement of mine shafts (geometrical wood truss construction) and the first mechanical and later steam-powered drainage/water removal allowed access to much deeper deposits from the very late Medieval period. This was particularly important because the sheer quantities of minerals required by the Industrial Era were an order of magnitude greater than anything before - that 100 tons of iron, in the 19th century, would build 1 kilometer of railroad track - without any locomotive, cars, and only a single track without sidings, switches, or signals. It took 10 to 50 times that for a single Ironclad, and so on.
Open Pit Mines (Modern and later) - once steam-powered excavating machinery (the 'steam shovel') and railroads are available, you don't really dig mines, you just remove the whole mountain to get at the deposits. Open Pit mines can be kilometers wide and a kilometer or more deep and virtually change the configuration of the landscape, but they allow exploitation of 1000s of tons of resources, once you expend the resources in machinery to get at them.
A similar 'progression' of Irrigation, chemical fertilizer and pest removal technologies could be posited for plant and animal resources so that, in most cases, there was a direct technological 'answer' to depleting resources. Where there wasn't, substitution of artificial materials for 'natural' resources could be invoked as a game mechanic: note that no one really needs Dyes, Ivory or Fur natural resources much any more: they were all among the earliest to be replaced by chemical (aniline dyes), plastics (bakelite, among others) and artificial fibers (rayon among the first). Of course, some of the replacement technologies simply move the Resource Problem to a different resource: aniline dyes are also called Coal Tar dyes because they are a derivative/by product of Coal, another potentially depletable natural resource.
The point, though, is that resources should not be Static. Now, you find all the amounts of a resource all at once, magically seeing them all as soon as a given trigger is reached. After that, they are unchanging and permanent - and, therefore, Dull. We have enough Dullness in the late-game of Civ already; there's no sense in regarding that as a Natural Product of the 4x game.
