The F-111 variant used by the SAC as a strategic bomber was designated FB-111A. Once they were replaced by the B-1, they were redesignated F-111G for use by TAC.
The Douglas A-26 Invader was redesignated B-26 by the newly formed USAF (resuing the designation of the Martin B-26 Marauder). But, when the upgraded B-26K Counter Invader was deployed to Thailand during the 60s, it received the alternate designation A-26B to avoid political issues.
Then there is the story that the SR-71 was intended to be the RS-71, but President Johnson garbled the designation during the announcement.