The error message appears if a job path is changed for an already configured and saved job.
It's a non-blocking warning and you can proceed with the change acknowledging the possible risks.
Changing the path does not necessarily leads to any problems with synchronization. However, on rare occasions some unexpected behavior may be observed if the new directory or its parenting/child subfolder is or has ever been used in this or another job. See particular cases described here.
It is safe to proceed if you're sure that this Agent and/or the new chosen path has never been used in the job before.