For Arria V device, the mapping of nPERST is as below:
- nPERSTL0 --> bottom Hard IP of pin_perst
- nPERSTL1 --> top Hard IP of pin_perst
In your case, try workaround it by changing to use Soft Reset Controller.
Using Soft Reset Controller doesn't required the connection to pin nPERSTL0. Tie pin_perst to 1 at top level file and nPERSTL0 can be left unconnected at pin assignment.
Steps to switch to soft reset controller in Qsys:
1) Edit the .qsys file
2) Search for the string 'force_src'
3) Set parameter force_src to 1:
<parameter name="force_hrc" value=0" />
<parameter name="force_src" value=1" />
4) Save the changes to the .qsys file and regenerate the Qsys system.
5) Use npor input to reset the core and application logic.