Before thinking about whether the duals are reasonable or not, I think you have to double check whether what you are doing is actually reasonable.
If I understand correctly, you a MIP problem M. You optimize that as a MIP, then you run solveFixed(), then you query the duals. Correct? As I already noted in that other thread, this will not give you the duals for M! It will give you the duals for a different model: M with all integer variables fixed to their current solution. Are you sure this is what you want for your column generation?
Since there is no appropriate duality for MIP, the pricing for column generation algorithms has usually to be done in the tree!
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