I performed IO PLL reconfiguration on Arria® 10, but the phase may be out of phase. Please let me know how to solve this problem.

After reconfiguring the IO PLL, be sure to reset the PLL by asserting areset. 
Please also refer to the following document.

AN 728: I/O PLL Reconfiguration and Dynamic Phase Shift for Intel® Arria® 10 and Intel Cyclone® 10 GX Devices 
(search for Resetting the PLL)

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Category: Specifications 
Tools: - 
Devices: Arria® 10