I can't guarantee this, but I'm pretty sure from what I've seen around here before that clearing a terrain type will NOT affect the future occurence of resources there. To the best of my knowledge, the resources are all 'set' at map creation, so square X,Y would already be designated to get rubber regardless of what its terrain type may be by the time you learn replaceable parts. Like I said, I'm not 100% positive on that, but I'm reasonably confident that it is the case.