There is an application note < AN 367: Implementing PLL Reconfiguration in Stratix II Devices > available at: /content/dam/www/programmable/us/en/pdfs/literature/an/an367.pdf.
Page 31 mentions a design example #3 titled < Implementing Phase Shift Stepping Using the ALTPLL_RECONFIG Design with Write Parameters>.
There is no link to this design example.
You can download the design examples from this link: Design files for Application Note AN367.