Forgot to add...

The last time it happened I deleted the account and then installed it again. I would rather learn to recover the emails the right way.

Did you look up the Trash folder of your POP account to verify if the missing messages have been erroneously deleted ? Since you are using message filters did you have a look in the target folders of your filtering ?

If you are unable to recover your missing messages there is a possibility to re-download all messages from the Inbox folder on the server. To do this you would have to delete - Thunderbird closed- the popstate.dat file which is located in the \Mail\pop.xxx.xx\ account folder in the Thunderbird profile folder. To open the profile folder you'd have to go to Help > Troubleshooting information > Profile Folder > Open folder... (then quit Thunderbird) Re-downloading all Inbox messages probably will create some ore many duplicates, depending on the number of messages. To avoid this I would first copy-drag the Inbox folder of your POP account in the Local Folders. After verification that all POP account Inbox messages are now stored in Inbox in Local Folders you can delete the messages from the account Inbox before deleting the popstate.dat file in the profile and restarting Thunderbird to re-download all messages from the server Inbox.

An alternative method would be to delete popstate.dat, re-download all Inbox messages and remove duplicates with the add-on "Remove Duplicate Messages" https://services.addons.thunderbird.net/en-us/thunderbird/addon/removedupes/ Unfortunately the latter only works with Thunderbird versions from 128.0 - 144.*

Well....

Sadly deleting the popstate.dat did not work. I moved all the emails still populated into another folder to avoid duplicates and all that was done is it indexed the emails moved to another file.

Forgot to mention. Its a gmail account.

Did you look up the Trash folder of your POP account to verify if the missing messages have been erroneously deleted ?

I did but not all the emails were in the trash.

Since you are using message filters did you have a look in the target folders of your filtering ?

If my filters had worked it would have deleted them off the host server too because I have the filters set to delete on pop server too.

Sadly deleting the popstate.dat did not work. I moved all the emails still populated into another folder to avoid duplicates and all that was done is it indexed the emails moved to another file.

This surprises me. I just made a test: delete about 100 messages in the Inbox of my POP account, quit TB, delete popstate.dat in profile folder and restart TB. All deleted messages were re-downloaded and the Inbox folder indexed.

Forgot to mention. Its a gmail account.

I've never used Gmail, so I don't know.

If the still missing messages are very important for you and if you haven't already compacted the Inbox folder you may try to recover them with the add-on "Undelete" https://www.ggbs.de/extensions/Welcome.html

Update....after about an hour the emails started to show up on Thunderbird.

Thank you!

There must have been very many: thousands ? Ten thousands? BTW: the "chosen solution" should be my proposal, not your update from today ....