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It will backup fine when done. However, if it is opened again after the backup then the .OST (at least in O365 commercial they use an .OST file) will become aged and if restored to this older version Outlook will complain that it is an older version and download all the contents from the cloud again.
If you are using some other .PST files, perhaps for archiving, then as long as Outlook is closed it will backup and restore fine. I do mine all the time, I also use a synch tool to copy my archive .PST files off to various encrypted disks for additional backups. I copy my .PST file to another PC as well, to insure that this archive .PST is kept up to date.
In short, as long as Outlook is closed it will backup the mail files. If you are concerned about the main. OST file, it will back it up too, but the backed up file becomes out of date immediately as soon as you restart Outlook and restoring just it (or the whole OS) will prompt Outlook to download and update the .OST file. You are already getting a backup of the.OST in the MS O365 cloud.