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If you replace the VXI-1553-IP7 with a VXI-1553, you need to change the initialization step and get new connectors.
The only software change is in the initialization. You need to change a few parameters in your call to BusTools_API_Init or BusTools_API_InitExtended. Any application you have running still works with the native board. The advantage is that the native card has 1 megabyte of memory (not 64K), and you can upgrade the firmware through the API. The native also is much faster than the IP, since it is not constrained by the 8 MHz IP bus.
Mechanically, the only real difference is in the connector. The native board uses a 15 pin D connector.