I believe I figured it out, and if i'm correct it seems the solution was simple, and also a little silly. In case anyone else notices duplicate database connections in their Table of Contents and editing workspace pop-up dialogue (upon starting an editing session), it appears that this is simply ArcMap misrepresenting database connections as separate connections when the data added from the database was added at separate times. If your map document saves one connection to database A and you later add another file from database A, it may appear in the Table of Contents (List by Source) as two separate connections. This seems to simply be ArcMap treating the connections as separate instances due to their being saved at separate times, and it may help to remove the duplicate connections and add all files at one time via one database connection to remedy the issue. Otherwise, you will have to stop editing some files in the database and begin editing the file from the duplicate database connection instance every time you want to edit both of those files, as it is treated separately in the editing workspaces. If anyone knows a better way to handle this please let me know. I'm currently running ArcMap 10.3, so this seems like a glitch that will hopefully be fixed in future releases/ArcMap Pro. Thanks!
