I passed the duplicate highlight along to others and got the following response:
I have looked at the logs as far back as I can and it appears that this user must have had these annotations created by an early version of the IOS Gospel Library with a bug that created duplicate annotations. The logs show that this user had over 3700 annotations on March, 14, 2012 (this earliest time we logged this information).
We had not seen this issue for a long time and I think this bug has been fixed.
So hopefully that explains why it occurred, and that it shouldn't occur any more.
As for the bulk delete option, we will keep it in mind for when we work on study notebook again.