You may encounter this error in the Quartus® Prime Pro edition software version 17.0 Update 2 and earlier when compiling design files that have been encrypted using the encrypt_1735 flow.
The problem occurs when compiling a design on a Linux operating system using design files that have been encypted using the encrypt_1735 flow on Windows.
To work around this problem perform a dos2unix conversion on each of the encrypted files.
This problem is scheduled to be resolved in a future release of the Quartus Prime Pro software.