I lost approximately 65% of my biotinylated protein after the second Zeba spin column. What happened?

It is unlikely that the protein is still on the column, as the resin excludes molecules with MW greater than 7,000. It is possible that you experienced some precipitation of your protein immediately after modification. If the protein concentration is too high (for some antibodies), aggregates can form and a precipitate forms. If this is the case, you might try lowering the Ab concentration to around 1 mg/mL. With some antibodies, lysine modification, removal of charged groups, can drastically affect solubility. If this is the case, you might try modifying with a lower MSR. Biotinylate your antibody again using a lower antibody concentration.