Will meat taste okay if I cook it in a pan where the leftover fond seems burned? I have found that after 2 batches of chicken breasts, the fond is in the pan for enough time to start burning, so the third batch gets a little black and starts to taste burned. 

Does it mean that I should deglaze or wash my pan every 2 batches to make sure I won't get a burned taste?
I'd deglaze the pan after each pan and transfer the juices to a small bowl to make a sauce 

I would wipe/clean (no soap) the pan after each batch.

After the last batch, transfer the bowl content and make a sauce with the last pan drippings and what you already have.