Unofficial Fallout 4 Patch

I probably should have elaborated and mentioned that Penny's Shop is staying locked during the daytime when you would normally be able to trade. The same is true of Jacob's office. I realize that it's deliberate for them to be locked between 8pm and 8am (or something like that).

Also, the save is attached now.

Hi,
Once i discovered the complex's location their (jackob, penny etc..) health bar turned in red and doors were closed, daytime, which seems to properly follow up a "story line" ?

I confirm that if you side with them (letting the synth getting killed in jail) everything goes back to normal...

Even if it does go back to normal after completing the quest (which isn't something I've tested for on the save I provided), I doubt it's deliberate for the shop to be locked during the day while the quest is active. When I went back to a previous save from the bugged save, her shop was open as would be expected during the course of the quest (and the same goes for Jacob's office). There has to be something causing the issue to occur. Whether or not it can be prevented or fixed is another matter.

This is why i added a "?. And this health bar becoming red while not being effectively hostile is very uncommon in the game.

My point: i can confirm your issue and i can confirm that everything goes back to normal once the quest ends (considering you side with Covenant)

DialogueCovenantScript.

The idea was to update the door status when the player enters Covenant location, then start a timer. While the player stays within Covenant location, the timer repeats at short intervals and updates the door status at opening and closing times.

Turns out now that the timer event never did anything with the doors. It played door closing scenes at closing time, but these scenes are "cosmetic"; they don't actually do anything with the doors.
At opening time, the script does nothing at all. Must have been forgotten ....

This is more complicated than it did appear at a first glance, because DialogueCovenantScript has no control on where the player is when it is supposed to change the lock status of the doors. If the player is in the shop or the office at closing time, he will get locked in until the next morning. Of course, you can still pick the lock, but if you're still at an early stage of the Human Error quest, you may not want to do that.

Conclusion is that we can't fix this properly.

RIght now, the actual lock states are only changed by the OnLocationChange() event that runs when the player arrives at Covenant. When this runs, he's still outside of the town walls, so there's no risk of locking him somewhere.
If you arrive during the night, the doors will be locked, and while you stay, they'll never become unlocked (because DialogueCovenantScript is not handling the actual locks, as already explained). If you arrive during day time however, the doors will be unlocked and never become locked while you stay.

So here's my compromise: DialogueCovenantScript unlocks the doors at opening times (in case the doors were locked when the player arrived), but does not lock them at closing times (so there's no risk of getting locked in the shop or office). Not perfect, of course, but the result is pretty much the same as what the vanilla scripts are doing when the player arrives at day time.