Hi Joanna_LaBresh, if your IgY is captured on the protein column, low pH should be able to elute the IgY VERY efficient. Key is you have to incubate the column in such condition for ~5 min before you start collecting the eluate.
If you have already done that, then the question is, have you followed the flow through/unbound fraction to make sure that the problem that you have is not because of the binding?