[Ryan M.]

Your idea should work. My team is doing it in basically the same way. Here's what I'd do.
commands.h

extern struct commands *command_list;

/* externs for the actual command lists */
extern struct command_list_1[];
extern struct command_list_2[];

commands.c

#include "commands.h"

struct commands *command_list;

/* actual command lists */
struct commands command_list_1 = {
   /* commands */
   {NULL, 0, 0, 0}
}

struct commands command_list_2 = {
   /* different command list */
   {NULL, 0, 0, 0}
}

user_routines_fast.c (at top of file)

#include "commands.h"

user_routines_fast.c (in autonomous function, before the while loop begins)

if(dipswitch == 0)
      command_list = command_list_1; // This makes the command_list pointer look at command_list_1. Because arrays in C are pointers anyways, this _should_ work... Should. :)
else if(dipswitch == 1)
      command_list = command_list_2;

Then, add the newly created commands.c to the project.

So yeah, your idea works.