Well, folks, I thought Angela at Intuit fixed the issue this morning for me.  She was able to get an acknowledgement for the husband's return (the one I submitted, but it was saying just "transmitted", but the IRS said they have it).  Then we deleted the wife's file from Homebase (scary!).  Then we restored from yesterday's backup.  It then showed that it had not been transmitted.  I changed the name of the husband's file.  Angela issued a credit for the processing fee on 3/16 that I was charged for wife's return (which was not transmitted).

So, then I transmitted the wife's return, which appeared and acted like a normal transmission.  However, I just checked for acknowledgements on that transmission (and I got one), but. . . . . . the acknowledgment had the husband's file name on it (yes, even the new file name) but the acknowledgment is attached to the wife's return, and the new acknowledgement number IS THE SAME NUMBER AS THE ACKNOWLEDGEMENT NUMBER THAT IS ATTACHED TO THE HUSBAND'S RETURN!!!

So, I don't know what the status is at this moment.  I will have my client check "Where's my refund" tomorrow afternoon to see if the IRS says they have received it.

And by the way, Angela said she had only seen this issue happen when returns were transmitted in a batch.  She had never seen it happen with pay-per-return.   I only transmit returns one at a time.  I am retired actually, and only process 15-17 returns a year.  And I don't even know how to copy with Windows or whatever that other person was talking about.