Why have academics switched from using BC and AD, to BCE and CE?

Because BC means “Before Christ” and AD means “In the Year of Our Lord.” Not exactly scholarly neutral, especially if you’re discussing other cultures, religions, or historical periods where Christianity isn’t relevant. 

So they switched over to “Before Common Era” and “Common Era,” which is a total fudge that doesn’t really fool anyone, but it’s enough of a figleaf that we don’t have to redo all of the dates.