FPLL reconfiguration will fail and the status register is stuck with "busy" in polling mode if either Icp/Loop Filter Resistance is reconfigured. FPLL reconfiguration will also fail and the status signal stuck with " waitrequest " in waitrequest mode if either Icp/Loop Filter Resistance is reconfigured in the Quartus® II software versions 12.0 and 12.0SP1.
The status register stuck in "busy" state in polling mode and the status signal stuck in "waitrequest" state in waitrequest mode, because the State Machine in the reconfig IP is repeating itself in a wrong state whenever Icp or BWCTRL is reconfigured.
This is fixed in version 12.0SP2 of the Quartus II software.