OneDrive Sync Client Should Pickup Company Name Change automatically
There's a high chance that a tenant can change the "Company Name" for various legitimate business reasons. Currently, OneDrive sync client acts weirdly in that situation by creating two separate instances (folder structures or whatever you call it) when users syncing a new SharePoint library. Very simply, OneDrive should be able to pickup the current name in Office 365 "Company name" attribute and replicate when it gets changed.
Alex M commented