Manually create a couple folders (or labels, being we are using gmail IMAP) called folder1 and folder2
Delete any message from the inbox, so it ends up in the “trash” folder.
Drag the email out of the trash folder, and drop into a folder1
Click on folder1, so you can see the email you just dragged there.
Click “refresh”. Voila! The email disappears right before your eyes. It will now only be visible in the “all mail” folder
There has just been a new eM Client (interim) Windows release version 9.2.1553 update on the release history page which appears to have fixed the email from dissapearing in the Gmail label (if you first deleted or moved the email to the Gmail trash folder) as in your steps above. This new update appears to have fixed this issue for me.
Note: - When I first tested this specific issue on the new update on two computers the problem still happened (only the first time) I tested it. Further testing after closing and reopening eM Client the problem never happened again. So close and reopen eM Client after updating as otherwise might still have some old eg: cache in the label.