Sounds like you have been using an Imap mail account in Thunderbird. You subscribe to see various server folders although all the default ones eg: Inbox, sent etc should be automatically subscribed to be seen in Thunderbird. All emails are stored on server and imap account subscribed folders synchronise with server folders of the same name to display the emails you have in those folders on the server.

If you have no emails in server Inbox because you deleted them via webmail account, when Thunderbird synchronised with server Inbox, it cannot display something that does not exist.

Imap mail account folders are not independent of the server.

Do you have a backup of your profile ?

General information about IMAP. https://support.mozilla.org/en-US/kb/imap-synchronization

Unfortunetly I had no backup.

I tried the steps I found online to reset the X-Mozilla-Status:0001 back to 0000 in the INBOX

...\AppData\Roaming\Thunderbird\Profiles\86o6qent.default\ImapMail\mail.optimum.net - INBOX, but that did not restore the emails. Shortly after that my computer rebooted so I fear I permanently deleted messages. I noticed after the reboot that the size of the Inbox was considerably smaller.

I compared my settings to the IMAP settings in the link provided and they match. However, when I had POP3 email I could delete the messages from the server and they would remain in my Inbox. The reason I prefer to delete them from the server is because older messages were constantly being re-loaded to my iphone even after deleting them from the phone.

With IMAP, how can I keep the messges in my Thunderbird Inbox and still delete them from the server.

re :With IMAP, how can I keep the messges in my Thunderbird Inbox and still delete them from the server.

You cannot. Imap Inbox can only show what is in the server Inbox. The folders are as if one and the same.

re :I tried the steps I found online to reset the X-Mozilla-Status:0001 back to 0000 in the INBOX Although you said you had no backup, you did mention still seeing emails in mbox files; it would have helpful to tell me about those mbox files still being available with email contents. The method you mention is used to change 'marked as deleted' emails from X-Mozilla-Status:0009 to 0001. It also would not work because you would have needed to exit Thunderbird to work on those files and when Thunderbird restarts, it would synchronise with server to show what is on server - there are no emails on the server. I would have advised you to do the following: get copies of all the imap account mbox files into your 'Local Folders' mail account. Then when you restarted those emails would appear in 'Local Folders' mail account as 'Local Folders' account folders do not synchronise with any server.

re :Shortly after that my computer rebooted Why ? That implies you allowed computer OS updates and just let it shut down everything and reboot without asking. Surely the computer must have asked if it was ok to perform a restart. I suggest you check some settings on that matter and force the computer to not do restarts without permission.

Thank you for your response and advice -- I will do as you suggest moving forward.