I'm not sure I understand what you're asking... System.owner is a relationship maintained by the system automatically which records which user created an object. I do not believe you can amend the content of this through a microflow.
Instead, if you need to be able to set an 'owner' of an record, create your own association between your object and account object, then you should be able to maintain it through microflows as you wish.
You cannot set the System.owner yourself. It is possible that the user that was originally the owner of an object was deleted. We do not clear System.owner references when a user is deleted because this would result in a huge amount of queries slowing the system significantly. The edge case where a System.owner no longer has an attached user is something you will have to take into account, the warning you showed is a result of that.
I suggest you update your question with some image to give everyone a better grasp of the situation....
But in general - you create a new object with a buttonaction from a datagrid that contains the relation with the parent. Which makes the connection automaticly.
If you delete a System.User (or an inherited Account) then all objects that have this user as their owner can give an error saying non-existing object.
A solution is not to delete but inactivate users.
And fixing the current issue can only be done in the database if you know what you are doing by changing userid 721 to an existing user id.