There can be odd enharmonic translations when transposing a chord progression to a new key, in particular if there are modulations within the song.
You can fix these issues manually by duplicating the song and editing it. 
In the editor you can "Set and Transpose" the song to a new key (what we call a Hard Transposition*) then correct any of the enharmonics and save.
This effectively locks the song in that key with the enharmonic chords written how you best want to view them.
We have not solved the complexity of enharmonics yet, but we have it on our list.
Many songs have temporary modulations from the original key or go through one or more key changes and determining where one key ends and the next starts is a very complicated problem to solve with algorithms. A good composer will introduce modulation in a very smooth and seamless way so that chords can ambiguously belong to one key center or another. Even detecting something as simple as a 2-5-1 can lead to false positives. When transposing, we decided to relate our enharmonic choices to the original tonal center which will lead to some incorrectness if there are modulations in the songs. You can use the editor to do a "hard" transposition and manually correct any chord symbols.

* Hard transposition iOS/Android:

* Hard transposition Mac: