Hey Kristen -- Sounds complicated, and I'm not sure I get all the details completely, but I've had similar experiences and started to notice the following, mostly with cards and layouts.
Scenario:
I have a card and use it in a mapping rule for a layout. Everything's cool, working as desired.
Now I want to delete the card (I'm resetting things for a demo session and want to start with no cards or layouts except for the defaults.)
If I delete the card first, I'll get the "Update Failed, Out of Date" message.
To avoid this or clear it, I need to delete all mapping rules in all layouts that call the card and publish all these layouts (without the card reference.)
Then I can unpublished and delete the card.
I follow a similar procedure for deleting layouts --
Set all collections so that none use the layout you want to delete
Publish all collections that are out of date.
Then you can unpublished and delete the unwanted layout.
Perhaps that's rather fussy, but it works.
I had similar experiences with articles and collections. If an article or collection is used in more than one collection, I would get a similar error. I had to work out which article or collection was used in multiple locations before I could unpublished and delete.
Hope that helps