That sounds a little extra messy. You are correct (as far as I can tell) that your return was not rejected. I would think filing a paper return or a amended return with a letter explaining everything that happened would clear it all up. Or call them back and if they say you need to provide a copy of the transcript of the return filed, explain about your issues with getting the transcript and that you're pretty sure it was filed with $1 in line 2b.
If none of that works, I guess you'll have to file a 4506-T to request a copy of the transcript by mail.
