You can do it by putting in a check that tests to see if a .txt file has changed. In your second instance of JMP, you can run a simple script that changes the .txt file.
First script
Names Default To Here( 1 );
Save Text File( "$TEMP/flag.txt", "0", replace );
For( i = 1, i <= 100, i++,
If( Load Text File( "$TEMP/flag.txt" ) == "0",
Wait( 1 ),
Throw()
)
);
Show( i );
Script for second instance of JMP
names default to here(1);
Save Text File( "$TEMP/flag.txt", "1", replace );
Jim