Everytime I have treated with Corid, I use the "severe outbreak" dosage for 7 days and then the "preventative dosage" for the next 5 days. I haven't ever taken a break while treating. I guess we all have our own ways of doing things.
As for integrating the 2 flocks of chicks. Are both flocks...
Looks like they're on their way to recovery! Continue to keep a close eye on them and their poop, etc. If any are still acting a little worse than the others, you can do a Corid drench to the individual bird. Corid is a thiamine blocker, not necessarily a medication, so just wash your hands...