As suggested by Tony, I've enabled message Archiving for the domain.

Since I've activated message archiving, new mails arrived, some are corrupt again, but they are in a good shape in the message archive.

2024-08-03 08:15:49.443 | DEBUG    | Verifying GRP file d:\SmarterMail\Domains\somedomain.ch\Users\joe.doe\Mail\Inbox\2024_7_28.grp
2024-08-03 08:15:49.443 | DEBUG    | GRP file d:\SmarterMail\Domains\somedomain.ch\Users\joe.doe\Mail\Inbox\2024_7_28.grp contains 4 entries.
2024-08-03 08:15:49.443 | DEBUG    | Entry UID: 2536 | start: 1208 | end: 6897159 | size: 6895951
2024-08-03 08:15:49.677 | DEBUG    | From: <eric.smith@foobar.ch> | To: <manu.guex@foobar.ch>

2024-08-03 08:15:49.677 | DEBUG    | Entry UID: 2537 | start: 6897159 | end: 13988440 | size: 7091281
2024-08-03 08:15:49.802 | DEBUG    | From: <eric.smith@foobar.ch> | To: "'joe.doe'" <joe.doe@foobar.ch>| Subject: =?iso-8859-1?Q?AOR_-_Cat=E9gories_VHC_et_VHRS_pour_2025?=

2024-08-03 08:15:49.802 | DEBUG    | Entry UID: 2538 | start: 13988440 | end: 13890775 | size: -97665

Traceback (most recent call last):
  File "C:\EvenSmarterTools\smart.py", line 837, in <module>
    main()
  File "C:\EvenSmarterTools\smart.py", line 795, in main
    check_accounts_integrity()
  File "C:\EvenSmarterTools\smart.py", line 649, in check_accounts_integrity
    grp_file_status = smarterlib.check_grp_file(grp_file)
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\EvenSmarterTools\smarterlib.py", line 284, in check_grp_file
    grp_file_content = f.read(grp_file_entry.Size)
                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: read length must be non-negative or -1

When you click on the mail, on the list, nothing happens, it just doesn't load that particular mail.

In my case, I was able to open the emails. I'd get anything between "[No HTML Content]" to lines and lines of HTML code instead of a rendered email.

I noticed my Domain's settings.json originally had an empty array for the "domain_aliases" parameter, but after renaming now has all of the aliases I added, so my issue seemed related to Domain Aliases.

        "domain_aliases": [
            "somealias.ch"
        ],

It is interresing though that you were able to fix the issue by doing a rename of the domain.

Side question: How are the affected users on your side accessing their mailbox. From IMAP ? From mobile phone/desktop ?

So to be safe, a "Reload domain" of all domains should be something to consider ?

Still, I'm not sure yet I understand the link between an issue with domain_aliases array in the domain settings.json and mail corruption.

# Load SmarterMail DLLs
from pythonnet import load
load("coreclr")
import clr
assembly_path = r"C:\Program Files (x86)\SmarterTools\SmarterMail\Service"
sys.path.append(assembly_path)
clr.AddReference("MailService")
from SmarterMail.Standard.Files.Grp import MailboxGrpFile

def check_grp_file(grp_file):
    # Check a GRP file for possible known issues
    # logger.debug('Verifying GRP file %s' % grp_file)
    out = None
    result, loaded_grp_file = MailboxGrpFile.TryLoad(grp_file, out)

    if not result:
        logger.warning('Cannot load GRP file %s. It seems invalid.' % grp_file)
        return False

    logger.debug('GRP file %s contains %s entries.' % (grp_file, len(loaded_grp_file.Entries)))

    for grp_file_entry in loaded_grp_file.Entries:
        logger.debug('Entry UID: %d | start: %d | end: %d | size: %d' % (grp_file_entry.UID, grp_file_entry.StartOffset, grp_file_entry.EndOffset, grp_file_entry.Size))

        if grp_file_entry.Size < 0:
            logger.warning('%s: Entry UID: %d has a negative size. start: %d | end: %d | size: %d' % grp_file, grp_file_entry.UID, grp_file_entry.StartOffset, grp_file_entry.EndOffset, grp_file_entry.Size )
            return False

        # Read group file entry content from file
        with open(grp_file, 'r+b') as f:
            # TODO: Read only header part (detect emtpy line?)
            f.seek(grp_file_entry.StartOffset, 0)
            grp_file_content = f.read(grp_file_entry.Size)
            f.close()

        # Process content and check for missing mandatory headers
        msg = email.message_from_bytes(grp_file_content)

        if 'From' not in msg and 'Subject' not in msg:
            logger.warning('%s: No "From" and "Subject" headers found in (at least) one message. '
                           'Could be an issue with this GRP file content!' % grp_file)
            return False

        logger.debug('From: %s | To: %s | Subject: %s' % (msg['From'], msg['To'], msg['Subject']))

    return True