Audio Sources/Custom Audio for existing scores
I posted this as a Improving MuseScore.com discussion, but I'll post it here too because it applies to both.
Currently, if you want to have custom audio for your score, you have to upload the score from the MuseScore app with that option selected, or you can take an existing score and use a YouTube link as the audio source.
If you don't want to delete and re-upload a score (losing all views, favorites and comments on the score) and still want custom audio you will need to export the score as an MP3 file which you must then put in an MP4 file. This file must then be uploaded to YouTube, after which you may finally use it as an audio source for a current score.
A way that could exist in theory is to upload a private score and use the MuseScore website's "Send to YouTube" option and use that as your audio source for the existing score, however, when MuseScore sends to YouTube, it only takes the MIDI data of the score and uses it's own soundfonts to generate the music in the video.
How to fix these issues:
1. When giving users the option for audio sources for their existing scores, give them the option to upload an MP3 file.
This seems like it's a good middle ground because the MuseScore application is perfectly capable of giving the user an MP3 file of their score with their soundfonts, and the MuseScore website is clearly capable of putting an MP3 as the audio source for a score (considering downloading the score's MP3 is an option)
2. When uploading your scores with custom audio from MuseScore to YouTube have it upload using their custom audio.
3. Let users of the MuseScore application update scores from the application itself.
This is currently possible if and only if you initially uploaded the score from the application itself. If you uploaded a score through the website, you will not be able to update the score using the application.
You could have the MuseScore application "fetch" the scores that the user currently has uploaded, or you could have make the users provide the link to the score they would like to update (have the application check that the link's score is from the user currently logged in so users can't change other users' scores).
This issue has been on my mind for quite some time hence the length and detail. If you read all the way through, I'm glad someone other than me at least knows.