I have this issue; in Office 2016 Pro Plus, in my favorites section I have moved all my inbox's from 6 email accounts in there and in a specific order. Now, for the past 2 months the inbox order is keeps rearranging itself and the default sent items, drafts and Archive folders are now at the top.

I've got my email accounts inbox order working now....nothing I've done but keep moving them back to the order I like. But, the Sent Items, Drafts and Archives folders still remain at the top. They used to be at the bottom. I've moved them to the bottom but on reopening Outlook, I'm back to square 1 again.

For a quick work around I've found that once you open outlook and see your order is wrong.....all you need to do is right click your outlook icon in the taskbar and open a new window and the new window will have your folder order correctly layed out.

This is OK but is there no real fix for this as it's annoying as hell.