Problem with Transposition

I have just bought installed the iPad version of notion and so far I'm very impressed. But the reason I got the software is because I have to learn a lot of jazz licks and being jazz, have to learn them in lots of different keys. So I got notion, plugged the notes in, all good. I transposed to the new key and then transposed back to the original key and now the notes I have are not the notes I started with. Lots of accidentals have gone missing so the notes have actually changed. I'm not talking F# is now Gb but rather that F# is now F. Has anybody else had this problem? I've taken a backup now of the score in case it happens again as I had to go through and correct all the notes.
Also, while I'm here I have to say that it would be great if I could just set a key for the whole piece. Then just select a new key when you want to transpose. You can do this for instance in "iReal B" and it's so handy. It's a bit convoluted in Notion having to select everything then transpose.
Many thanks all and like I say, all in all it's fantastic software!! Thanks!!
Also, while I'm here I have to say that it would be great if I could just set a key for the whole piece. Then just select a new key when you want to transpose. You can do this for instance in "iReal B" and it's so handy. It's a bit convoluted in Notion having to select everything then transpose.
Many thanks all and like I say, all in all it's fantastic software!! Thanks!!