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I mark animals in large numbers all the time, just to this point not birds, especially immature with lots of growing to do. If no side effects per original querry, then labor and retention are most important considerations.
Need to be able to distinguish as many as 18 broods / matings repressented by 100 chicks at a time. Leg banding is labor intensive and would have to be repeated several times as chicks grow. I also have mulitple cohorts at 4 week intervals making leg banding even more problematic. Wing bands to be applied at 4 weeks as they are cheap with good retention and enable ID of individuals. Permanent marker marks if need be will be applied again at 2-week intervals to compensate for poor retention but that will still be much less effort than leg banding which is reserved for adult broodstock where ID without handling to done from distance.
No ill effects, but marks must be reapplied at frequent intervals. Sometimes only days, because of fuzz shedding.