Two chicks died, moved remaining to new coop but they won't go in at night

First time caring for chickens. I got 6 chicks about 6 weeks ago. I was told they were 3 weeks old at the time. We got them from our neighbor who has free-range chickens who spend a lot of time on our property. Two of them died without an obvious cause last week, and I have a question about the behavior of the remaining group.

Since we got them, they have have been in a good-sized yard that is fenced in, and there are two coops in the yard. The people who lived in this house before use kept chickens, but the whole area has been empty for 3 years. When we got the chicks, we cleaned out the yard - weed-whacked the overgrowth, and put new straw and sawdust in both coops.

They seemed to naturally gravitate toward one of the coops, so we used that one at night. The first 5 weeks were great and their behavior followed expectations. By the end of the first week, they were going to the coop at night on their own, and I just shut the door at night, as advised by my neighbor to protect them from predators. They had clean water and were being fed a starter feed.

One week ago, two of the chickens were very sadly dead when I opened the coop in the morning. The others were fine. I didn't see any signs of trauma or anything unusual on the dead bodies or in the coop.

I disinfected the waterer, replaced all the hay in coop, in case something was making them sick.

That night, the remaining 4 would not go into the coop. Unsure what to do, I ended up putting them in the other coop in the yard (which they had not used yet) - which I'll call the "second coop" for the rest of this post.

Luckily, the next morning they were fine. I was hopeful that we could just start using the second coop. From the research I wondered if mites were the issue, but
I couldn't see any signs of mites in either coop. I also didn't see any of the physical symptoms of mites (no scaly legs or de-feathered areas) and the two who died were not lethargic or acting sick the evening before they passed.

I used DE liberally in the second coops and on the chicks themselves.

The neighbor from whom I received the chicks said she has never had any issue with mites and no issues with the other chicks in the bunch except for one baby who died very early.

Here is my question: they seem fine in terms of behavior and appearance. But it has been a week, and they still are hesitant to go into the 2nd coop at night. I had hoped that it would just take a few days for them to get used to it, but they are still resistant to going in at night and it's a fight to get them to go in. Aside from this, their behavior and appearance seems normal.

I am not sure what to do next. Am I doing the wrong thing to keep trying to get them accustomed to the second coop?

Sorry for your loss! Heartbreaking no matter the age, My only experience with a similar behavior is with older chickens. Earlier this spring, my 8 year old Wyandotte died during the night. Old age. She was roosting with 5 Seramas. To this day, those 5 Serama hens will NOT sleep on the same roost. They witnessed her die from that roost. I would have to guess your chicks witnessed the death of the babies. Just a thought.

Thank you so much.
I thought about that as well - but they are in an entirely new coop. Maybe they are still associating their loss with nightime/roosting?
I'm just not sure if I should try to move them again (I'm not even sure where) - if something like mites might still be an issue.

Chicks4Pgh said:

Sorry for your loss! Heartbreaking no matter the age, My only experience with a similar behavior is with older chickens. Earlier this spring, my 8 year old Wyandotte died during the night. Old age. She was roosting with 5 Seramas. To this day, those 5 Serama hens will NOT sleep on the same roost. They witnessed her die from that roost. I would have to guess your chicks witnessed the death of the babies. Just a thought.

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I had to use a "night light " to get chicks in at night as chickens can't see well at dark. You might have to do that ( mine was on timer) could use a solar something or, catch them and place in coop on roost for a bit. I closed mine up for 10 days as babies so they would know that coop is " home" so they may be confused about that too. I'm glad there's more losses for you welcome here .