Some audio interfaces are capable of performing src on spdif input, which is what I think you mean. Many DAWs however, as I mentioned earlier in the thread, are capable of doing both in and out src on the fly, so one option would be to leave your audio interface at 48k. Whether that's a good option for you depends on the reason you're using 96k.
This would be so much simpler if the Axe-FX had selectable i/o sample rate .
No, i mean on output. Recording the DI into the AXE over SPDIF is easy cause of SRC. I'm talking about reamping, you have to get that signal BACK to the axe, over spdif, and that's where it's hard to do the SRC on the output