In that case my next suggestion for a fix would be to reinstall Mail, but as far as I can find Mail is not available as a stand alone download. That leaves with two alternative suggestions...
  1. Boot from the Recovery drive and reinstall MacOS or...
  2. Boot from the clone and clone it back to your normal boot drive then restore any files that were changed since the clone was made from the Time Machine backup.
Personally I would choose number 1. Neither fix will solve the mystery of why the mailboxes disappeared in the first place, but either could save you days/weeks of sleuthing to find the cause which could have been an isolated event such as a bit getting switched from zero to one (or vice-versa) by some transient event.

By-the-way is Abby Roade your avatar?

PS: As an afterthought, just in case the problem is with your boot drive I would take a look at the S.M.A.R.T. values for the drive and, if it is an HD, run a surface scan just to be sure the drive is healthy.

Last edited by joemikeb; 11/06/18 09:09 PM. Reason: Ad postscript

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