Thanks all for your valuable inputs. I have seen patches on scoby earlier as well but this was an unusual one. I agree with Anita that since it has overgrown in a normal looking one it should be harmless. I actually have two batches in parallel and both had same growth and both look similar now. Today I bottled the liquid and started 2nd fermentation stage. I am going at make use of these scobies in a new batch and see how it goes.