After 68.8.0, all of my mailbox folders are unavailable. Had to revert back to 68.5.0 to get them back. (Restore point)
I can see the .msf files in my ...\Mail\Local Folders. Left pane is completely blank (no inbox, trash, etc). Right pane is also blank, no contents. View/Folders/All is selected. Also lost all of the calendar features.
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I don't believe 68.8.0 has new changes that would have caused your problem - the new changes are dated April 30 in https://hg.mozilla.org/releases/comm-esr68/pushloghtml
.msf files are not necessarily the only thing needed to display folders in the pane. Do you also see the mail folders themselves, your address books, etc in the profile directory?
Also, when you start Thunderbird what do you see in tools>developer tools > error console ?