[Zubersoft]

I'm really not sure why you are seeing those performance issues. How many pages is that 100 MB PDF? The PDF library should only be embedding and modifying pages that were actually changed, not all of the pages. I might need to have you export your song to .msf (right-click the song, click Share->Export as .msf and share the .msf with mike@zubersoft.com) so I can see if I can reproduce the issue you are describing to see if there is a potential solution. 

As far as the deletion issue, select the annotations individually (either with the selection tool or the layers window) and then you can delete them directly without using the eraser tool.

Mike