I am still not sure why my audio software glitched on exporting last night’s episode. The lesson for me is to listen a little more closely to the encoded files before uploading. I usually skip through one of the files, just to make sure nothing is obviously wrong. Clearly I skipped right over the missing parts without noticing.
I opened my original project back up, re-exported and checked the output file more closely. I’ve uploaded freshly encoded files that I am now certain have the parts that were missing from the files I posted last night. I’ve updated the post for the episode here on the web site and tweaked the feeds so the fixed episodes should re-download automatically if you are using a podcast specific client.