No, you cannot use dynamic reconfiguration to switch from XAUI to PCI Express Gen 2 in Stratix® IV GX and GT devices due to a problem with Quartus® II Software Versions 9.1 to 10.0-SP1.
If you attempt to use dynamic reconfiguration to switch from XAUI to PCI Express Gen 2, the PCI Express interface will only operate in Gen 1 mode.
Using dynamic reconfiguration to switch from PCI Express Gen 2 to XAUI is not affected.
This issue will be fixed in a future version of the Quartus II Software.