This is exactly why I tell folks to not file any amended return until after their originally filed return has been processed, and they have physical possession of any refund they may be due on that originally filed return.
While an e-filed return is processed almost 100% by computer, an amended return must be processed by hand, by a human. This can take anywhere from 6 weeks, to "never" (literally!).
When an amended return is received and the originally filed return has not been completely processed, the human handling the amended return has no choice put to set it aside until after the originally filed return has completed processing.
Since the amended return is in an actual "hold" box, it may sit there for weeks, or even months before the human gets back to it; and thats "if" they get back to it. To reduce the probability of that happening, you shoudl wait until the orginally filed return is processed and you have physically possession of any refund due on that original return.
