I do not believe it is possible for ProSeries to "pick up a file from a different directory" for e-filing.   Whatever file has been selected by you is what is transmitted.

A return does not need to be rejected to be amended.  In fact, if it was rejected then you would have the ability to correct the information before resubmitting.   

It is NOT possible to submit two returns for the same SSN (taxpayer) without one of the returns being rejected.