nothing to worry!
i would consider it as the best feature of IRCTC!
if you have more than 2 berths (1 upper and 1 lower) and if u cancel the ticket of pax who was allotted lower berth, u wil automatically get lower berth showing that the pax whose ticket u cancelled was initially allotted upper berth!
yesterday I cancelled berth no, 1, 2...
more... in train 12956! we had booked for 5 i.e 1,2,3,4,5. Autimatically the one who was at 3 got no. 1 berth (lower) and berth no. 2,3 were cancelled!