Importing and Exporting Alpha Channel

Hi,

I have a Flash video (FLV) with an alpha channel (I don't have access to the original QT video). I used Adobe Media Encoder to convert it to Quicktime to import into FCP X to make a quick edit and export back out. How do I ensure that the video imports into FCP X with the alpha channel and exports back out with the alpha channel? I set Adobe Media Encoder to encode the alpha channel, but how can I tell if it imports into FCP with the alpha and exports back out with the alpha? Is there a way to check that in FCP? After I exported it out of FCP, converted it back to FLV and imported it into Flash, it no longer had the alpha channel. Not sure where I lost it along the way. When I exported out of FCP, I chose Apple ProRes 4444.

What things do I need to make sure I do in each of these converts, imports and exports and how can I tell if the alpha channel is there in FCP X?

Thanks,

Brian