I think I figured out the issue. I was trying to edit my entries in Paperpile, knowing that if I edit the local copy then it won't end up correcting my own copy of the entries. I wanted to collect all of the entries for this bibliography in a single folder in Paperpile to make it easier to edit them. So, I opened the local copy of all of my references, exported them back into Paperpile and created a folder while doing that. Big mistake! That made a second copy of all of my entries. I thought I could then just merge the duplicates and edit them. But those edits don't propagate back into the google doc. I suppose the link got broken when I merged the duplicates. So, now I get to go through the whole document and re-enter all of my citations. It would be nice if there were an easy way to group all of the references in a single paper into a folder so they can be quickly edited in Paperpile. Each time I try to quickly edit references I screw something up. Perhaps I should just look up each reference individually and correct it instead of trying to be fancy. It would be less time consuming in the end.