You probably have settings in the new config which are not being overwritten by your old config. For example, if you have "r_drawviewmodels 0" in your new config, but not "r_drawviewmodels 1" in your old config, replacing the new with the old will not set your viewmodels to display again.
You would have to reset your TF2 to default, and then put the old tf folder back, then it should take it back to where it was before. I just did this after messing with a crosshair switcher.