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1.2. Individual Messages Are Missing from HelpSpot

Updated: 21 Aug 2026, 12:35 PM EDT

Use these troubleshooting steps when mail is flowing normally but specific emails aren’t making it into a HelpSpot inbox. See Email Has Stopped Flowing into HelpSpot for when no emails are making it into a HelpSpot inbox at all.

1. Did HelpSpot receive the message?

When HelpSpot successfully imports an email, it leaves two traces: an entry in the Audit Log, and the message itself moved out of the inbox. 

With Archive Mail disabled, that means a normal move to Deleted Items; with Archive Mail enabled, the message moves to the helpspot_archive_folder.

If a missing message has neither trace, HelpSpot never saw it, and the cause is on the mail platform side. 

Specific to Microsoft 365: HelpSpot performs a normal delete and cannot place a message in Recoverable Items. A message that landed there was hard-deleted by something else. 

Common culprits in this scenario:

• An old or duplicate HelpSpot installation still polling the same mailbox over IMAP — it deletes mail this way, and creates the tickets in its own database. Worth ruling out after any server migration. Also check that no obsolete IMAP mailbox connections are still enabled on your production install.

• A mail client or admin tool running automated filters or delete jobs.

• A security product retroactively removing the message. Microsoft Defender ZAP and automated investigations do not appear in the mailbox audit log, which is why audit searches come up empty. Open the full message trace detail for one missing message and look at post-delivery events.

• Non-interactive sign-in logs in Entra ID will show any leftover process polling the mailbox over IMAP4, with the source IP.

2. Was the message received and rejected?

Check the Rejected Emails figure on System Health. The usual cause is loop protection working as designed: HelpSpot stamps every message it sends with an internal header, and if a message carrying that header arrives back in a mailbox HelpSpot fetches, it is rejected rather than turned into a request.

To trace one, find the request referenced in the rejection and look at the customer email address on it. If that address is one of your own configured mailboxes, or an alias or distribution list that delivers into one, that is your loop. 

The fix is to make sure mail reaches HelpSpot from an address that is not itself a configured mailbox. See New Request Loop Protection.

3. Was it sent somewhere unexpected?

A message that was imported successfully can still seem as though it’s missing. Before digging further, check whether a Mail Rule routed it to a category you are not watching, deleted it, or marked it as spam, and check the Spam and Trash filters.

If You Still Need Help

If none of the above resolves it, submit a support request and include as much of the following as you have:

• The System Health report (Download report for support on the System Health page), or the output of php hs health.

• Your helpspot.log file, or the email-related excerpts if it is very large. For more detail, turn on debug logging temporarily first.

• The sender, the recipient mailbox, the timestamp, and where the message ended up in the originating mailbox.

• Whether anything changed recently — an upgrade, a server migration, a patch window, or a mail platform change.

Knowledge Tags

Missing Email  /  Troubleshooting  /