Ah, shoot. Oh well.
The only solution I can think of for the Hatchery issue is to go through the full questline again and select a different answer at the last leg. I think whether you get Hatchery’s Secret #3, #4, or #5 is determined by whether you select “Search the Incubators”, “Inspect the Security Console”, or “Activate the Security Console”. Not sure which gives which, though.