Does anyone know if I import a video that is closed captioned, then work with the file and export it out if the portion of the file that contained the caption will still have them in the exported file and/or mini dv tape?

What kind of file? What format is it in?

The video is originating from a Beta SP tape, and will be exported to either a quicktime file or mini dv tape via firewire.

If you capture and stay in a format that is 720x486 it will work. The only reliable way is to use uncompressed. Once you go to the dv codec which is 720x480 you will be cutting off the lines with the CC.

Also if you insert any video you'll also be erasing the CC.