Ok i think i have found the issue here. I have configured udld mode aggressive on all the ports. So that is why when i admin down the port on SW3(e3/2-RP), the Root switch port SW1 (e3/0) goes into err-disable state! Since Root Switch port e3/0 will not receive any traffic, it goes into err-disable state. Finally, i just needed to bounce it, to work as before.
Also, when i tried to admin down the port on the Root Switch (SW1-e3/0) i noticed that the far end port doesn’t go to the error-disable state, even though the far end port (SW3-e3/2) is configured with udld mode aggressive. But then i remember that this should be expected, since i am admining down a port on a Root Switch, and the root switch is not sending BPDUs ever, so that is why SW3-e3/2 doesn’t go also into err-disable state!