Just went back into the program and the contents of all folders have gone even though it says the messages are there at the top. I exited the program, restarted it and now it appears to be working normally, except for one folder which is still missing over half its emails.

Your screenshot Shows that you have enabled the Quick Filter and the Filter 'Show only messages from people in your addressbook'. Note the small blue bar.

Thanks. Turned off searches in address book and made no difference. The emails are still in All Mail. Tried dragging them or copying them to the folder and that doesn't work, presumably because the folder thinks they are already there because it says a much larger number is in the folder than actually showing.