Multiple setups on one 7i96 board

I have a dual purpose homebuilt machine,have always had a router and plasma cutter set up for each on earlier versions . Upgraded to 7i96 board and want to know if this is still possible.or would I need to flash the 7i96 every time I change?

I do not know the exact configuration of your machine. But if you wiring it just a little cleverly, then I think there's no reason to reflash the configuration.

setups basically the same only some i/o pins are used in one but not the other

You just need two different configs, no flashing required.
 

You might be able to run a single config and use the multispindle feature  with the router on Spindle 3
Se how Plasmac uses the engraver as an example.

Note that you can use multiple configurations without reflashing the 7I96
by first flashing the alternate firmware to the fallback location, then you can
switch firmware by selecting the desired firmware via mesaflash:

Choose primary configuration:
mesaflash --device 7i96 --addr 10.10.10.10 --reload

Choose alternate configuration::
mesaflash --device 7i96 --addr 10.10.10.10 --fallback --reload

But you probably don't need to change the firmware. If it is all the same machine then just use a number of INI files (one for each machine arrangement) all in the same config folder.

My milling machine can operate as a horizontal mill or a vertical mill. Or a gear hobber, and with 3, 4, or 5 axes. I do this by having several INI files and a selection of shared or unique HAL files for each configuration. They all share the same tool table, but different .var files.

Joint.0 can drive stepgen.5, for example, so it's just a bit of HAL tinkering to swap axis allocations around.