That is by design. As @Gary advised in the following thread post, if eM Client automatically cleared the read messages after being read in the GUF, “it would be a cascade effect” where the next message would then be read and then automatically dissapear and so on.
So if you had a eg: long email you might not then get a chance to read it all and it dissapears after whatever X time you set in Settings / Mail / Read, and then you have to go and find it again.
So that’s why you need to click out of the unread global folder to clear the read messages.
That may change one day, but that’s how it works for now.
External Sync: When I read an email on a different device (mobile/webmail), eM Client correctly syncs the status (the email un-bolds), but it remains listed in the “Unread” folder.
If you are “still highlighted on the Unread folder at the time when the status is changed to read on another device”, you will also still normally “have to click to another folder and then click back to the Unread folder” to get it to change status, as it may not change status otherwise “depending on how long the read status takes to sync back to eM Client” from the server mailbox.