Having loaded 2,048 IRs at the user slots cannot mean that you are actively using 2,048 IRs at your presets! I have 342,197 IRs at my hard drive, but I do not use more than 10 or 15 at my active presets.
If implemented, and you really want to keep 2,048 IRs loaded at the Axe-FX, you have two options: 1) do not apply that upgrade 2) Organize your presets and user IRs. The ideal way to do that would be using the "Export Preset + CAB bundle", to safely link the presets with the user IRs. I hope that it will be implemented soon at Axe-Edit.