How does TB count email messages?
The total number of messages, displayed at the lower right-hand corner, never matches the list of messages I see on screen. Who is counting, and where are the missing messages (not drafts, trash or archives)? Some replies are nested, but not enough to make up the difference.
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Try repairing the index folder. right click on folder and select 'Properties' click on 'Repair folder' button click on OK.
Do you compact folders on a regular basis to remove the hidden 'marked as deleted' emails? Note: if you suspect any corruption of the folder in question, compacting can cause a loss of emails, so suggest you move all good emails out of that folder into eg: Local Folders Inbox. Then try compacting the folder. right click on folder and select 'Compact'.
Just had a thought - If you are using via 'Menu Bar: 'View' > 'Folders' > 'Unified' or via Mail Toolbar : 'Menu icon' > 'Folders' > 'Unified'
Suggest you try: via 'Menu Bar: 'View' > 'Folders' > 'All' or via Mail Toolbar : 'Menu icon' > 'Folders' > 'All' to test to see if the count is correct.