It is correct that regular allergen tests don't work for degraded or hydrolyzed proteins. That is because most antibody (ELISA) tests require that there be two antibody binding sites on a protein molecule for detection to occur. When the protein is not intact, those binding sites can become seperated, preventing detection.
There are tests that you a competitive assay format. The competitive format only requires one binding site, and can work well with hydrolyzed protien. It is important to realize that these testes generally should not be used for qunatification (no matter what the test maker says). There are no reliable hydrolyzed protein standards, and standardizing against intact protein is misleading.
Any test that you use should be validated to work with your matrix system. Ideally, this could be done by spiking the food with known amounts of the target analyte and looking at detection and recovery. However, this is again complicated by the lack of an appropriate digested standard. Validating against intact protein can be very misleading.