To do a flock treatment you need to turn the pump off for 12 to 36 hours to let everything settle. If you didn't quite kill everything and there is some small patch of algae that is just holding onto life in a biofilm somewhere, turning off the pump is the best thing that could possibly happen for that algae. No circulation means that it only has to deal with the chlorine in the water right next to it's self, instead of all the chlorine in the pool, so the algae will have a much much better chance of recovering.
Most green algae isn't that hearty, most of it is usually dead well before the FC level holds overnight. But if the pool has been closed for a while and the algae has had time to really settle in and build biofilms, or if you are dealing with some of the heartier kinds of algae, then you have to be absolutely through and never give it a moment to even think about recovering.
Overall a flock treatment isn't likely to cause the algae to come back, but there is some risk.