I maintain 2 folders in Mail - Devonthink In and Devonthink Sent which I use to temporarily park emails to be imported into DTPO for backup, as opposed to those I want to keep in Mail but which are of lesser importance and do not require backup to DTPO. I move those emails from my Inbox and Sent box folders temporarily to the DTP In and Sent boxes only to import them in to DTPO. They are then returned to the Mail boxes. I have been doing this at least weekly for a number of years, neveer with a problem.
Today, I moved emails to each of the folders and then started to import into DTPO. I imported those in the Devonthink In. DTPO then appeared to hang although I could see the emails had been imported into DTPO. I then attempted to stop the import.I suspected that DTPO was trying to sync at the time. In the end I had to Force Quit from DTPO. The emails in the Devonthink Sent Mail box had disappeared. I restarted in the hope that this might restore the emails but it did not do so. I have tried to recover them from Time machine but cannot locate them.
Strangly, the emails in the Devonthink Send box had not been selected so I am surprised that they have been deleted, somehow.
Running OSX 10.12.6 and Mail 10.3, DTPO 2.10.