My understanding was that they used a lot of General Lees ... numbering in the hundreds, and that only a handful were in more than one episode.
I was watching one of the cable shows where they poke around old warehouses and junkyards and such and they found a guy who had 3-4 of them ... all wrecked.
In fact, I heard somewhere that by the end of the final season, they were using some other make and using different camera angles to sort of disguise the fact. The supply of 1969 Chargers had dried up.