If the only thing you did was rename the database file, that should not have broken the links. The thing to remember with external storage is that FM creates and maintains the directories it needs and you should not mess with them outside of FM, e.g. "moving files around to various locations". I suggest you go back to a version that was OK and start again.
(PS. that expression is "to all intents and purposes" )
Container fields should never be touched by anything but FileMaker. I've made this mistake myself and regretted it.