Microsoft has struck again with an untested update that was released in the last two weeks, and has resulted in a substantial amount of postings and complaints from users. Many with duplicating emails in their Outlook and others with deleted emails.
Microsoft has acknowledged the problem, in terms of when a fix will be released that is still undetermined.
Microsoft’s acknowledgement of the problem.
https://community.office365.com/en-us/f/158/t/433332
There are some fixes you can do until Microsoft releases an update.
I took the option to revert back to Outlook 2016 (16.0.6366.2068).
There are plenty of examples on how to do so, Please read all of the comments to find your work around.