Stephen,
For an upload the spacecraft remembers how far you got through the upload process. It stores the file offset for the last byte that it received. When you login and request to upload of the same file on the next pass it tells you the offset number to start from. The ground station software should then begin uploading from that point. So in theory it should complete over several passes as needed.
One common issue is having too much uplink power so that you can't receive while uplinking. The full duplex nature of the channel means that you need to be able to receive responses from the spacecraft when your receiver might be desensitized. So make sure either your antennae are isolated enough or you are not using too much power. 10 -25 watts should be sufficient into a yagi.
But tell us a bit more about the setup you are using, Which software, tnc, radio, antenna and we can try to help.
73
Chris
73
Chris