There is a UI bug in the Move dialogue window which misleadingly shows the incorrect folder, for example:
The destination folder is My folders > Test but looks like it is the Inbox folder; with the Archive folder list expanded you would not even notice that the Test folder was selected. @ModTeam
To locate the missing emails select an email, then Move, and see which folder was select; for the above example the missing emails where all located in the Test folder.
Thank you for explaining that so well - I helped on a similar case the other day and knew that is what happens, but couldn't word it properly! That is why I generally do drag and drop - I have umpteen folders and it is no fun to choose the menu option and use the Move dialogue window. Also, the Move dialogue seems to remember the last time I used it and pre-select the prior option.
Another option is to check your Sort By settings (and maybe View settings). See if that brings it up to where you want. Do a test with an expendable email (trash it, then try to recover it) and show us some screenshots of what happens (obscure any personal information, of course).
Set up an email client like Thunderbird which has an easier to use search function. It might be that it is not lost, just hidden in the pile somewhere.