Constructors do not return to finish building if scared off.

[King Doom]

Give a constructor a few things to do and if a pirate or whatever has them trying to escape then they will just abandon the thing they were working on completely and then move on to the next project on the list when they stop running. If you aren't careful this can cripple you as they waste massive amounts of stuff half building mining stations that are never completed.

[Canute0]

I am surprised that the half builded base was still alive after the Constructor escape. Normal the enemys destroy them.

[King Doom]

It happened roughly eight times before I noticed. I settled a massive really resource rich system, the kind with twenty planets and fifteen moons. I sat a fleet there and set my constructors to building. A single pirate ship flies in, constructors panic, fleet wipes pirate from existence, redo from start.

[Icemania]

King Doom, I'm not going to defend what happens on Auto, as all I have is distant memories of frustration.

If you play manually you'll get an alert when you are under attack so pause, go to the system, organise defence ships or pay protection temporarily if the Pirates are too strong. Move constructors away only if needed and when the threat clears send the Construction ships back (or cancel the protection agreement).

[Fishers of Men]

I manually control my construction ships and I set them NOT to flee when enemy ships are in their system. When an alert sounds, I go to the site and evaluate the situation. The enemy might frighten off the freighters(which I can't control that) but not my constructors until I give them orders to escape.

[kheben]

or you can go to the constructor design and set the stance to "flee when attacked" instead of enemy sighted

[Starke]

Agreed with above posters, if you don't mind checking out the situation yourself when a constructor is threatened, set to never run and make the call yourself, and 'flee when attacked' should allow your fleet to defend while allowing solo constructors to get away if you'd like to stay more hands-off.