Why are flagged emails disappearing from inbox and where do they go when the flag is deleted?

Have found the beast: Under the "View" tab is an item called "Enable Message Filter" - when ticked it automatically moves read messages from the inbox, leaving them in the individual email box [inside the Inbox folder]. I can only assume that this was enabled in an update - I simply had to "Disable Message Filter"

Thanks, the problem is limited to the inbox folder: once an email has been opened it stays there until I click on any other box or quit Mail. It is then visible in the individual email provider's box and Flag box if I have flagged it. So, not lost just (inconveniently) not in the inbox folder.

I can live with that, but would love someone to come up with a solution

Have just upgraded to Big SUR and it has changed my Mail preferences again. Now when I flag an email it disappears into the "Flagged" box. As I us my inboxes i.e. "All Boxes" I want to retain the messages with flags in there so that I constantly see them, rather than having to think, 'do I have any flagged mail', and then check.

Have tried rebuilding twice now and no change. Actually have three different email accounts: Optusnet (primary account); Exchange and iCloud. I normally view them all in "inbox" which is now only showing unread mail. If I go to the individual email accounts (sitting inside the "inbox") I can see the read, unread and flagged messages. So it appears the problem is with the "inbox" now only showing unread mail. A bit of a pain having to switch through the individual providers' and flagged boxes once a message has been read.