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Your daddy dog that was from a merle/merle breeding and came out normal is no more likely to have or pass on problems than any other merle dog. All "normal" merle dogs have a single copy of the gene, regardless of what their parents carried. A double merle that was born with no eyes...
Don't kick yourself. Accidents happen. I would like to suggest that if you keep the litter please don't put def/blind ones down. I have a double dapple dauchsund that was born with no eyes (dapple same as meral) she is 14 yrs old and I have had her since she was 8wks old. She has lived a very...