I think by the time you're ready to let them meet without a fence in the middle, they should really be well acclimated just from being exposed to each other for so long, so I anticipate that integration should go fairly smoothly, especially with extra clutter and space to utilize.
I think worst case scenario you're looking at putting them together once the run is expanded. Ideally you'd want for the adults to start losing interest in the babies before they begin mingling, but after 3 weeks of exposure I'd expect them to be close to that point anyhow.
Photos of your set up would help. How much clutter is there and how many feeders are available for the birds to use?
3 days is pretty short for see but don't touch, 1-2 weeks of continuous exposure would've been better. At this point I'd say keep the chicks in a fenced off area in the run (or...