If its real chamois then it probably didn't have much cushioning in it to start with.Its probably just worn away by constant rubbing
Cheaper synthetic chamois pads have a thin layer of foam sandwiched between layers and will get compressed in time.
You can buy replacement pads or better still send the shorts away for a replacement chamois to be fitted . (Impsport)
Unless you are really attached to these shorts you would be better off investing in a new pair, after all it is the main point of contact with your bike critical for comfort.
but like they say its your a***