yes there can be odd enharmonic translations when transposing (you might notice it also in using the automatic transpose in Practice as each chorus plays in a different key.)
If you regularly play a song in a specific key, duplicate it then in Song Edit change to that key in song Info (Set and Transpose) then correct any of the enharmonics then save. This effectively locks the song in that key with the enharmonic chords written how you best want to view them.