Separation depends on how severe the injury is. Obviously an open would that other birds are picking at would be a time where you'd want them completely physically separated. However I always keep separated birds in full line of sight of the flock (the exception would be contagious diseases, however if the bird was already in the flock, it's very likely that the disease has already been spread through the group).
I had one bird in isolation for 6 weeks. Her isolation cage was in the center of the run. Adding her back to the flock was as simple as opening the door and letting her out. It may not always go that smoothly, but chances of success are much higher when the flock still recognized her from having seen and heard her during that entire stretch of time.
Yeah I only figured it out by watching how much picking went on an hour after application, 3 hours after, 6 hours after, etc. If the picking is pretty bad, applying twice a day might be necessary to get results at all, but it's really not a good long term solution.
Adding birds back in is generally the same as adding new birds - abouty 1-2 weeks in a separate see-but-no-touch enclosure in full sight of the others, then optimally some supervised time together in a large enough space (like your run) with plenty of clutter to help distract and to provide hiding spots. There's different nuances with adding small chicks to adults, or a rooster to all hens, or younger pullets to older ones, for example, but the above is a general fits-most-situations type approach.
