I recently had to make a change to my POP email settings which caused my Windows Live Mail to re-download all of my inbox items. This is roughly 1500 messages. It didn't replace the current messages but added new ones to my inbox so I had roughly 1500 duplicates.

To delete these duplicates I went into the message store folder at
C:\Users\<user>\AppData\Local\Microsoft\Windows Live Mail
and deleted the emails that were updated Today for the "Inbox" directory of that mail account.

The problem is that Windows Live mail still reflects that I have 3k messages and the duplicates still exist while viewing my inbox. They now however say:

Message cannot be found
The contents of this message cannot be found.
Windows Live Mail

How do I refresh the Inbox view so it reflects my current emails, removing the 1500 emails that "cannot be found?"

A system restore seems a bit drastic. Would that even remove email files? The date column within WLM? that wouldn't sort by the emails I need (the new emails are dated the same as the old email send dates). I was able to delete all the duplicates as they were dated as modified today but my problem is they still show up in my inbox after I deleted them.

They read in my inbox as

Duplicate Email 4 - Today
Email 4 - Today
Duplicate Email 3 - Yesterday
Email 3 - Yesterday
Duplicate Email 2 - A week ago
Email 2 -A week ago
Duplicate Email 1 - A month ago
Email 1 -A month ago

so sorting by date isn't going to do any good.

note: I backed up all my duplicate emails to a different directory on my computer just in case I needed to put them back in.

I ended up exporting my mail folders (it only exports good emails) and then deleting that mail account, recreating it and re-importing.