Unread messages not visible.

New user of Macs - about a fortnight, and having issues, not so much with using the MacBook, but trying to work out why and where to find things. Latest issue which started this morning is on downloading messages from my POP3 account, I get 3 unread messages, but not visible anywhere. I read through the other discussions and checked my mail folder in library and found the messages, which were legit, not spam. Moved them to trash and checked the count on the inbox and they had gone. Later in the day i logged in again and have a similar message of x messages, 3 unread - mail folder in the library has different messages this time. Also with the unread messages comes (but not always) and blank header - so there is a dot in the first column to indicate a new message but the remainder of the line is blank, and the preview pane tells me to go to the server to read the message - however there is nothing in webmail server, inbox is empty since it has all been downloaded to MacBook.
Any thoughts or hints?

The problem is probably that the mailbox has lost the .mbox suffix in the filesystem, but you appear to have introduced new issues by tinkering with the contents of ~/Library/Mail/ without taking the index into consideration...
Report the names of the files and folders present at the first level of the ~/Library/Mail/POP-username@mailserver/ account folder in the Finder.
In order to post the exact file names and avoid typing mistakes, proceed as follows. In the Finder, go to ~/Library/Mail/POP-username@mailserver/. With that folder open, if you’re looking at it in View > as List mode, first collapse any expanded folders so that the Finder only shows the files and folders at the first level. Now, do Edit > Select All (⌘A), then Edit > Copy (⌘C), and paste it in your reply to this post.
Note: For those not familiarized with the ~/ notation, it refers to the user’s home folder, i.e. ~/Library is the Library folder within the user’s home folder.

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