Unless you care to do it like in the olden days where indeed people sat day for days and painted over such stuff frame by frame, it would likely be best if you simply duplicated the sequence, masked out a suitable area and moved it into place. This usualyl works sufficiently for stuff like skies or uniformely colored areas even if the damage is relatively large. Of course fine details would require different treatment and you may indeed face soem tedious manual labour, but that's impossible to judge without actually seeing your imagery.
Mylenium