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I don't believe there is any worry about losing any emails if you are seeing in multiple places. I am currently using Outlook.com and the Windows 10 app and seeing the same emails. In the W10 app go to the left navigation pane, and way down at the bottom is a gear wheel for settings. In the settings you can go to Manage Accounts, choose the account, then Change Mailbox Sync Settings. I have chosen Download Email from "any time" and I can search for and find emails back to when the account was created. Personally, I prefer the Outlook.com web interface to Outlook 2016 installed, and I access emails that way. There are both new and old interfaces for Outlook.com. In the upper right on a blue bar I see "Try the beta." The beta is nice looking, but lacks some of the functionality of the older version and some of the available settings. You should be able to still enter "outlook.com" in your Edge browser and go to your web-based Outlook.com email. Just bookmark it.
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