Quicktime X file disappear after convert it.

I have a video on .mp4 format, open it on Quicktime X then use the "save as" option to convert this file to an iPod format. Usually takes about 30 minutes. The weird thing is that if I leave the computer running the process and get back later, the file disappears.
When the conversion starts generate an icon on the desire destination. But apparently if you don't manipulate the file right after the conversion is done the file just disappear.
Does anyone had the same problem before? Any Idea how to solve it?
The thing is that I don't want to sit in front of my computer to wait until the conversion is done, just upload several video and used them once they are all ready.

Hi Brian
thank you so much for your help !
I still don't fully understand waht really happned...
But I think the problem was solved...thanks to you.
I firstly tried to do exactly what you suggested: Exported the project as QT, then quited FCP, dragged the file into Compressor's Batch window, told the compressor to make a MPEG2 frm it... and here it stoped working...Submit ws subdued and I could not make it work...Then I took a look at the file QT had exported...it was a 303Mb FCP movie, not a QT.mov file, and the sequence was about 4.5 Gb !
Here I tried something else:
First, from FCP, Printed the sequence to video. Then captured it to FCP again to a new project, through Log and Capture, this time it did not need rendering and in the Capture Scratch folder after saving the new project was a QT.movie file; Dragged it to Compressor and made a MPEG2 file...
On the phone with the project's author I heard for the first time the original QT.mov files he gave me were in fact exported from iTunes under MacOS 9.2...I don't know if this can mean anything, since I have worked before with QT files exported from iTunes with no problem...
Can you please give me your insight about all this ?

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