This achievement requires a bit of patience and preparation.
As you’ve noticed while playing, as long as the comms station is manned, you get a warning about “Incoming enemies” prior to being attacked. You’ve also noticed that before you’re able to use a beacon for jumping to another area you need to charge the engines.
To do this as painless as possible you need to get to a beacon that allows you to jump to a new area, charge the engines and WAIT!. After a while, most of the time you’ll get the enemy’s alert. Once you get it simply jump to a new area and you’ll get the achievement.
You could also get this by jumping to another area even if the enemy ships have already spawned. Keep in mind that the number of enemy ships dictates the charging time (more ships = longer charging time). As your commander levels up he gets a “fast charge” skill which lowers the charge time. That should work too.
It’s easier to sync up at the beginning of the game. Use the waiting time to heal crew members or fix the ship.