It sounds like one of those "gotchas", maybe.
The clip sent to STP audio file should show up in the timeline and browser as "clip name.sent". When you did the first send, did you save it to your HD? Have a duplicate sequence open that you went back to and couldn't find the sent clip so you then re-edited?
It may have been a work flow thing, or just a bug. It sounds like once you got the repaired clip on the timeline you had no problem round-tripping.
Here are a couple of interesting things I found:
1) since I have done repair work non-destructively, ie: reference audio, the waveform in FCP shows the original clip, even though to the ears it has been fixed, the waveform doesn't show it. That threw me for a bit.
2) once when doing multiple processes in audio file project and going back to it the next day (after saving and shutting everything down), the audio dissappeared, just vanished! So, I now make a habit of saving, then flattening all actions, and saving with a new name. Just a little PYA.
Cameron Young