If any admins are looking, I have filed a bug report as well: #362472, with a couple of samples for you 
I have seen a number of older threads on this topic, but nothing in the past 3 years.
I am trying to use DEVONThink 3 to archive my email from AppleMail. I have what I think is a lot of email - 28 years of corporate email, a couple dozen Gmail accounts, a ProtonMail account and an iCloud account for good measure. It’s taking up about 60GB on my main hard drive, and it’s high time that I archive most of it and move it to an external drive.
I currently run DEVONThink from my main drive, with the databases on an attached NMVe SSD drive. The databases take up quite a bit of room, so I want those offloaded as much as possible as well.
Now, I tried importing in the past for my corporate account, and therefore have an Email database that has some old mail in it. I was able to move this to another database I created (Overflow). As I’m looking at it, the structure is a bit confusing, with two names for the same email account (let’s say Foobar and Foobar2), with Foobar encompassing 8/2017-1/2020, and Foobar2 encompassing 2/2020-today. The mailbox structures are different, since they were different at the time of importing. It would be nice to have those consolidated somehow if possible.
Structures are basically Overflow>AppleMail>Foobar (with a number of subfolders) and Overflow>AppleMail>Foobar2 (with a number of subfolders, some of which are different from those under Foobar), and then what appear to be smartfolders (with a gear icon) for All Images (empty), All PDF Documents (empty), and Duplicates. The Duplicates folder has email spanning from 1999 through the present, though I did not specifically allow replicants.
My goal is to have a single Email database that is “clean” and contains everything.
The Email database seems to be special/protected in some way, since when I try to do anything with emails, the Email database opens, even when I have purposely NOT opened it so I and just deal with moving mailboxes around elsewhere.
Currently, I’m trying to move everything from the Email database to the Overflow database, so as to start fresh in the Email database. However, when I try to move a large (600MB) mailbox from Email to Overflow, DEVONThink hangs.
There must be a better way … I’m hoping those of you with a lot more experience with this than I have might be able to offer some assistance!
Thanks!
Steve