When using Altera_PLL_Reconfig, the translation logic from C logical counter to C physical counter may map incorrectly in the Quartus® II software versions 13.1 and earlier, causing the IP to reconfigure the wrong physical counter.
Disable the ADV_NETLIST_OPT_SYNTH_WYSIWYG_REMAP assignment in your project. Current versions of the Quartus II software must have this assignment disabled in order for C output counters to be updated dynamically. The IP is scheduled to be enhanced in a future version of the Quartus II software to allow you to use the ADV_NETLIST_OPT_SYNTH_WYSIWYG_REMAP assignment and dynamic reconfiguration of the C output counters.
You can refer to AN 661: Implementing Fractional PLL Reconfiguration with ALTERA_PLL and ALTERA_PLL_RECONFIG Megafunctions (PDF).