Just wanted to say that I have had this exact same issue with Outlook 2016 for Mac since I installed it on my 2016 MacBook Pro a few weeks ago.
My email is hosted with my website hosting company, Fat Cow, so in case anyone thinks it's associated with iCloud or gmail or something like that, I have proof that it happens with an independent email server.
I have spoken to Microsoft on the phone about it a few times recently, most of the time I share my screen with them and they check things and maybe even trash my plist file. But so far, nothing has cured the issue.
I noticed that there was an update for Outlook recently, just after I spoke with a Microsoft tech support person. I installed the update, and for a few minutes it felt like maybe this update was going to fix the issue.
But, no such luck. After a little while, there went the error message, there went my folders, and there went my hope of being able to use rules again.
If I didn't want to sort my email and put it in the appropriate folder automatically (as I have since the beginning of email, if I recall correctly), it wouldn't bother me so much.
But since I DO want to have emails appear in the appropriate folders, I sure would like to be able to use those rules again!
Please, Microsoft, do something about this obviously widespread error!
thanks!