My audio files are approximate 1 hour long, but the software only converts about 20 minutes of the file, and the remainders are cut-off. How to work this out?

SWF file format has a limitation of maximum frames. If the audio file has more than 16000 frames, about 22 minutes if the framerate is 12, the remainder of the audio will be trunctated.

If your audio file is longer than this limitation, you need to select output file as FLV (Flash Video) format in the "Publish" panel, FLV does not have a limitation on file length, and the audio quality is same as SWF format.