FWIW: Had a requirement to access an older e mail and lo and be hold found that about 90% of my e mail folders were BLANK. Could find no common thread as to why a few folders still had e mails but most were blank, ie: dates, subject, e mail account, NOTHING.
Plugged in my last back-up drive OSX 10.11.x ( I know I know) and all was well. A little search on the Apple support forum found that OSX 10.12.x created this issue in Mail. A very simple solution was to select the blank mailbox folder and hit "command L", which I guess disabled the mailbox filter. The messages magically appeared. If the folder happened to be one of the ones that had e mails in them, then the mails disappeared, so I am not sure whether one is disabling or enabling. Who cares??? Got my e mails back and my heart rate back to normal.
Daryl