On several occasions I have down loaded the charts in the AIP. When planning the trip they are in the memory. After shutting down the iPad and restarting for the trip the AIP charts have disappeared. Have I some incorrect settings?

Perhaps those plates have been replaced by the issuing authority? That is the only reason, short of manual intervention on your part, that a plate you have previously downloaded (where it will have turned green) will revert back to a white, un-downloaded state.