Thanks for the updated log. I only see one mail check in it, and this is what I see:
2014.07.25 16:28:26.553 -1000 AquaMail [IMAP.206] Sending: kman21 UID SEARCH UNSEEN UNDELETED
2014.07.25 16:28:26.700 -1000 AquaMail [IMAP_RAW.206] Data is <49>:
* SEARCH 8974 9690 9770
kman21 OK SEARCH done.
2014.07.25 16:28:26.700 -1000 AquaMail [IMAP_RAW.206] Line: * SEARCH 8974 9690 9770
2014.07.25 16:28:26.701 -1000 AquaMail [IMAP_RAW.206] Line: kman21 OK SEARCH done.
2014.07.25 16:28:26.701 -1000 AquaMail [IMAP.206] Result for kman21: 0 SEARCH done., traffic: 49 read, 36 write
2014.07.25 16:28:26.702 -1000 AquaMail [IMAP.206] Unread message count: 3
2014.07.25 16:28:26.702 -1000 AquaMail [SYNC.206] Adjusted command batch size: 25
2014.07.25 16:28:26.703 -1000 ImapSyncByCountStrategy Loading at most 25 messages from INBOX
2014.07.25 16:28:26.703 -1000 AquaMail [SYNC.206] The account's sync deleted is true, delete plan is 0
2014.07.25 16:28:26.704 -1000 ImapSyncByCountStrategy Creating a fetch check command for 1 to 8
2014.07.25 16:28:26.704 -1000 AquaMail [IMAP.206] Sending: kman22 FETCH 1:8 (UID FLAGS)
2014.07.25 16:28:26.852 -1000 AquaMail [IMAP_RAW.206] Data is <311>:
* 1 FETCH (UID 8974 FLAGS ())
* 2 FETCH (UID 9690 FLAGS ())
* 3 FETCH (UID 9692 FLAGS (\Seen))
* 4 FETCH (UID 9694 FLAGS (\Answered \Seen))
* 5 FETCH (UID 9712 FLAGS (\Seen))
* 6 FETCH (UID 9754 FLAGS (\Seen))
* 7 FETCH (UID 9766 FLAGS (\Seen))
* 8 FETCH (UID 9770 FLAGS ())
kman22 OK FETCH completed.
The server is reporting three unread ("unseen") messages.
The data returned by "SEARCH UNSEEN UNDELETED" and actual per-message flags are consistent with each other: check the UIDs, they match.
There is no reason for Aqua to "fix" anything, the data is consistent.
To reiterate: there are no inconsistencies wrt. unread message state in this log. The server reports three UIDs of unread messages, and their individual state is unread too.
There are errors with the server being unable to return message data, so this is some sort of corruption, and it has to be dealt with not by posting here, but by calling the mail service's support and presenting evidence from the log file:
1 - messages marked read in web mail being reported unread over IMAP
2 - server not being able to return data for two of your messages
I will also address these:
>>> "finger pointing is not helpful"
Did you have to use a loaded expression, "finger pointing"?
Working with a debug log, and discovering something wrong with a mail server / service is not "finger pointing".
It's debugging (in the broad sense) to figure out what's wrong.
When I see that the issue is with the mail server, well, am I supposed to take the blame just to be polite?
>>> "The server is actually saying it is corrupt"
Yes, there is something wrong with your account / messages / server's database / cache / index file / whatever else may be causing it.
Again, nothing to do with Aqua. The server is unable to return message data for two messages.
The IMAP commands are valid -- they may be different from those used by Thunderbird, or Outlook, or K9, or CloudMagic -- but IMAP is a rich protocol.
The server has no problem responding to those commands and returning message data for all messages but two.
And so it's black and white. Something's wrong with the server / service / cache / index file /... and should be fixed there.
>>> "graceful degradation on an error"
The IMAP protocol does not have error correction. There is no redundancy, extra information, as with error correction coding (and "graceful degradation" is something else entirely, actually).
You know that the two messages for which the server can't return message data are marked read in web mail.
But what if they were marked unread, and the server was returning them as read?
The exact opposite of the current scenario?
It's easy to see that there would be absolutely no basis for Aqua to assume that those "NO Cannot open" messages are either read or unread.
>>> "the client(s) put me in this corrupted state"
The client did not put anyone, anything, anywhere in a corrupted state. You're doing the finger pointing now.
There is absolutely no evidence that Aqua somehow caused this "corrupted state", and no reason to think that it did.
Further, since a mail app does not access a mail server's database / index / cache files directly -- and works by issuing IMAP commands -- then, by definition, any corruption is the mail server's fault.
Note that I'm not agreeing that this corruption is somehow caused by Aqua. There is absolutely no reason to think so, and no evidence to support this fantasy.
>>> "Correlation is not causation"
Exactly.
So when Yahoo let their SSL certificate for SMTP expire...
.. and when Apple broke SASL PLAIN authentication for IMAP
.. and when Office 365 broke all kinds of IMAP authentication
.. and when Gmail stopped sending those five-minute keep-alives for push mail
.. and when O2.pl was not returning any unread messages after a server "upgrade"
... ..... ..... ....
Since there were people using Aqua with those mail services at the time, was all of the above also caused by AquaMail?
While we're at it, let's not forget the hurricanes in Florida and the earthquakes in Indonesia.
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PS - Not trying to tell you what you should and should not do... but you might have had the issue resolved by now, if you contacted the mail service's support.