The D/S written on your I-94 stamp stands for "duration of status" and means that CBP authorized you to remain in the US for as long as you have valid J-1 status. This contrasts with most other I-94s which show a specific expiration date. If your valid J-1 status will end later than originally planned, you are still authorized to remain in the US until the end of your status and grace period.
Note that having or extending your valid J-1 status depends both on your DS-2019 end date and on continuing to perform your J-1 activities. If you stop doing your J-1 activities, your status becomes invalid even if you haven't reached the DS-2019 end date.
Regarding your question of whether CBP knows about your DS-2019 extension, in theory they should know, but in practice you can never be sure. It's always a good idea to carry documentation in case they ask, including DS-2019(s), printed electronic I-94(s), and offer letter from your J-1 program sponsor.