[McAroni]

If you just swap the file, the annotations should remain. At least at android.
You could try. To Make a copy from your song with annotations and swap the file there. But there should be no difference. 

As a side note: you should swap the via the swap file dialog.
Long press a song -> press the three dots-> swap file. 
If you  swap the file with in the "file" dialog of the song you will loose your annotations.