Did you mean that due to washing and further processing for 2nd target antigen is the reason?

It can be happen but I thing you have to select which target you want to detect first. Also, you need to consider which antigen you want to detect by DAB and/or others. I hope you can be able to balance by optimization and able to make your desirable data.

If you use two different target antigens, your staining should not be affected unless perhaps you don't stain for both simultaneously (i.e., in the same washes). If you do each separately, one may be more washed out than another. I do a 3-step permeability solution, wash in blocking solution, keep in blocking solution with all primary antibodies 24 hours, then rinse and introduce all secondaries simultaneously on the second day (working with NeuN and Iba1).

If you combine two chromogens for double-IHC, you should stain "with" the more resistent at the beginning. A common combination is DAB-Peroxidase-staining first followed by a red chromogen-Alkaline phosphatase-staining.

DAB can hardly be removed from the section. Some red chromogens are sensible to alcoholic washes.