From the end of June, Google will replace "duplicate" folders and files with shortcuts.

When items are replaced with shortcuts, the following will happen:
- We will remove items that are now in multiple locations from all but one location, and replace the removed items with shortcuts.
- The replacement decision will be based on the original ownership of the files and folders, and will also take into account access and activity in the other folders to minimise potential disruption to partnership.
- The replacement process does not affect sharing permissions or ownership of files and folders.
- The process is automatic and does not require the Username to do anything.

More information at https://support.google.com/a/answer/10686746 

A few weeks beforehand, Google will inform users via a banner in Drive.