Bryce K. Nielsen
Look at page 7 of the rulebook:
4. Check Pilot Stress: If the ship just executed
a red maneuver, place one stress token near the
ship. If the ship just executed a green maneuver,
remove one stress token from the ship (if any)
and return the token to the miscellaneous token
supply (see “Stress” on page 17).
After you reveal the dial, set the template, move the ship, then you check if you add or remove the stress token. So the test from the shuttle would have happened after the ship moved.