Due to a problem in the Quartus® Prime Pro edition software version 17.0 and later, you may see the following errors when using preserved periphery logic in a root_partiton.qdb file
Error (16045): Instance "<instance name>" instantiates undefined entity "<entity name>"
Error (16185): Can't elaborate user hierarchy "<instance name>"
Error (16186): Can't elaborate top-level user hierarchy
These errors can occur if the original project includes child partitions, or if the project includes HSSI IP. The HSSI IP creates a default auto_fab_0 partition.
If the instance in the error is a child partition that you have created, remove the child partition.
Otherwise, if the error references the auto_fab_0 partition, contact Intel support.
This problem is scheduled to be fixed in a future version of the Quartus Prime Pro edition software.