The filenames and path is what you entered each time you pressed render (I do the same: just select with mouse batch of clips and then select next batch and choose loop region only).
If these are MPEG2 HDV files then I believe Sony should be able to smart-render them. Open these files in a new project and match project property settings. Then choose matching HDV output when you render to final file.
If these are not HDV files then it's tougher. There are several MPEG2 join programs available but don't have any recent experience with these (see
http://forum.videohelp.com/topic265916.html).
Another option would be to output the files to uncompressed AVI if you have enough disk space for the project (about 900GB for 1 hour uncompressed AVI and 450GB for Sony YUV). Then open the AVI files again and render these to final MPEG2 output.
