To keep everyone updated, I may have had a solution from VIP Support which I have tested this morning.
Repairing different folders, such as Inbox and Sent items, and also rebuilding everything via the command line had not fixed the Conversations (threads) issue in Drafts.
The next thing they recommended was to add the account again, keeping the old one too (i.e. keeping both). The new one didn’t have the Conversations issue and the Drafts count was correctly lower than before. It looked this morning as though this may have solved the issue without much pain.
I unticked “Include when sending/receiving emails” for the old account but it still seemed to be checked, so I unticked “Exchange web services” too and then it was hidden. So I’m now running off the new/re-added account and seeing how it goes.
So far, re-adding my account has resolved the problems but I’ll let people know if they come back.
I also see emails in the Drafts folder and there is no way to delete them. They stopped accumulating after the last update to 10.3.2412.0. But I still don’t know how to get rid of them, and I have several hundred of them there. /dbrepair does not help.
The newer versions of eM Client no longer had the issue with incorrectly saving multiple draft messages, but… I was stuck with the many drafts from the older versions of the software. When I’d looked into my account using webmail (Office 365), I saw the multiple drafts were not present there, only within eM Client. So that told me I didn’t need to clean up the account itself. I did try different database repair options, but they did not solve the problem.
As you’ll see from my post above, VIP Support then recommended I add my account again (i.e. having two versions of the same Office 365 account). The newly added version did not have these accumulated drafts anymore, so it was safe to remove the older, originally-added account and just keep the newly added one. It’s been fine for me ever since.