I've not tried this, but I wonder if putting the shared function (and the shared function alone) into a file that is #inlcuded with the ISR and main would help?

Making the function static should avoid name clashes - and the ISR and main would have to be in separate files; something like:

shared.c
static void shared_fn( void )
{
   // your code here
}

isr.c
#include shared.c // Creates a *local* function

void isr( void ) interrupt x using y
{
   // your ISR code here

   shared_fn(); // Calls *local* function

   // more ISR code here
}

main.c
#include shared.c // Creates a *local* function

void main( void )
{
   // your main code here

   shared_fn(); // Calls *local* function

   // more main code here
}

Thus both main.c and isr.c have a "local" function called "shared_fn" - they are completely distinct, so no MULTIPLE CALL TO SEGMENT problems, and you avoid risking the Gotchas! of 'C' macros.
Downside is, of course, increased code size.