I had a similar difficult time with 2 different aged flocks once and did exactly this. Over time it seemed to build courage for the weaker chicks in each flock which is a good thing, and eventually when I mixed them permanently, it went so much better! Enemies became allies, lots of new friends, this should work for your groups too.To make this explanation a little easier I've decided to 'name' the two separate flocks I seem to currently have. Eventually they'll all be one flock (I hope) but since there are two batches of chicks (the incubator chicks and Sweety's chicks) in two separate runs being raised differently things are a bit crazy.
The two flocks are Sweety's flock, the 7 and 5 month olds w Sweety's chicks. Then there's the Tractor Supply (TSC) chicks which are the 10 and 11 week olds which also includes the incubator chicks that are still penned in the run with TSC chicks. I hope that makes sense.
I've tried for several days to integrate the TSC chicks with the incubator chicks, but a few of the older chicks just keep harassing them so I decided to try a different tactic.
Initially I wanted to toss the more aggressive TSC chicks in with Sweety's flock and let them figure it out, but that was just frustration getting the better of me and would put Sweety's chicks in danger as well as the 4 more aggressive chicks.
What I decided to do was . . . over the past few days I've been alternating which group I let out of the run:
I would let the TSC chicks out of their run and the incubator chicks could come out of the pen (into the run) and get some exercise without being harrassed.
The next day I would let Sweety's flock out of their run so Sweety could get more comfortable having her chicks out without them being harrassed by the TSC chicks.
This is working out well so far since I'm comfortable with Daisy being loose with the TSC chicks, but on the days Sweety's flock is out I keep her in the house or on leash when I bring her in the yard.
I'll keep this up the rest of the week and plan to let the two flocks out at the same time this weekend when I'll be able to observe them and see how things go.