Changing BAR configuration

We have an existing Qsys PCIe design running in an Arria II GX. We need to change the number and size of BARs and we cannot get Qsys to recognize the changes. We should be able to close the PCIe IP compiler block, assign addresses and return to see correct addresses, but we always return to see the same addresses and BAR sizes. Is the scripting behind QSYS stuck? Do we need to start over with a new qsys file and recreate our system?