After doing the dance over the years between Dispatch, Spark, Airmail, I eventually defaulted back to Mail.app, over stability issues.
I’ve long since forgotten which ones were the culprits, or the specifics, but suffice it to say that at the time, certain things happened that went beyond simple crashes (possibly similar to @MacSparky’s issues of trying to reply to mail X, but instead having the reply sent to mail Y)…
Regardless, I’ve been on Mail.app for over a year again, and despite it’s shortcomings, it remains predictable, and doesn’t do anything out of the ordinary.
Except for making me work twice/thrice as hard! 
It’s possibly a case of me being too impatient/quick, when I am triaging, and not allowing enough time to sync, but want to check if this happens to anyone else?
I have 60 unread emails by the evening.
I work through the list, either deleting or flagging, but mostly swiping to have Read.
At the end of it all, I might have 25 unread emails.
The next morning, I have 90 unread emails.
Before going in to work, waiting for the coffee to brew etc., I triage again.
I clear out the new emails… before starting to recognise some of the emails again, and then realise I am now having to triage emails that I know I worked through the previous evening…
As in, emails I had marked as read (the deleted ones, have stayed ‘deleted’), are back, but marked as unread.
And since I triage by working through unread emails, the fact that the sync, of these having been marked Read last night (for whatever reason) never carried through, means I am having to deal with them again the next morning! 
That happen to anyone else?
Starting to get a bit annoying now.
To the point of my thinking about putting my dancing shoes on again…