Boy, I don't know.
Rule of thumb(which are by no means carved in stone) is that nests should be lower than roosts, so they don't roost(sleep) and poop in the nests.
You could leave them there and add a 2x4 or 1x3 across the perches for easier access to the nests...and if they do sleep in them, move them then.
Personally I'd move the nests down and/or the roost up.
I made my nests at a height easy for me to reach, (bottom of nests are about 24") with a perch and ramp for the birds ease of access.
Then made roosts about a foot higher, which actually made the roost board an easy height for me clean also(board about 36" roost 8" over that).
Hopefully you used screws to install your roosts and nests...I use deck/drywall screws for everything, easy to drive and easy to change things.
I did a lot of planning before building and still had to change stuff after coop was in use and I saw some issues.
When I was building mine it was on here every night trying to get as many ideas as I could, but then I ran out of time. I kind of under estimated how fast chickens grow. I think for slapping it together pretty quick it turned out alright. I knew there would be a learning curve, it seems like I am out there every night tinkering with something. I have to get my poly up on the sides of the run this weekend. Do you poly your run, or do you just lock yours in the coop all winter? It seem like 50% of the people I talk to lock them up. When I poly the sides should I leave the whole south side open? My other question is how did you get your birds to switch over to the nipple waterers? I put a bucket in the run with some vertical nipples until my horizontal ones show up, I don't think they have touched them.