Im pretty sure that, everytime you save a part in pro/e, it'll save it as .prt.1, .prt.2, etc... So as SrGillberto said, make sure your Pro/E session is cleared, and find the one you want. Save it. That'll will beomce the most recent save. When you open the assembly, pro/e will take the .prt saved most recent, hence the .prt.1 and so on.
Hope it helps.
Using WF3.0, and WF5.0