If the bookmark or index entry doesn't have a number of pages indicated, this could create large files that are not needed or even crash the app.
For this reason, you should enter the number of pages of a song if you want the flatten/bounce to work properly.
Choose Bookmark This Page from the Do menu:
Then enter the number of pages the song is in the PDF
Create a new index or edit an existing one:
Choose your index or choose +/Verify and create or edit an index.
In the index editor, enter the number of pages in the corresponding field for each entry.
In the above case, all songs are 1 page long (circled in green). But if they were more than one page, you would see 2, 3, etc for the number of pages.
Once this has been done, all of the share commands should be much faster and reliable.