A mailbox I imported to EagleFiler from Mail contains 3232 records.
I sorted the mailbox by Tag Names, highlighted the messages in each Tag Name group (noting the number of messages each contained) and exported the messages.
After importing the mailboxes to Mail, there is a total of only 3218 messages.
By comparing the mailboxes in Mail with the Tag Name group in EagleFiler, I can see some of the messages that are missing but don’t see anything suspicious, although of course maybe that’s because I don’t know what to look for.
(In case it matters, I had originally exported the mailbox using macOS 10.14.6 and am now running 10.15.3.)
Any idea why some messages shouldn’t be re-imported?