Description
Due to a problem in the Quartus® II software versions 12.1 and earlier, you may see this error when compiling a design containing transceivers and using incremental compilation.
Resolution
To avoid this error apply the following assignment to your project:
set_instance_assignment -name PLL_AUTO_RESET ON -to "<hierarchy>|altera_pll:altera_pll_i"
This problem is scheduled to be fixed in a future release of the Quartus II software.