I recently removed an attribute from an object knowing that it was referenced in a number of places that would require manual changing. I ended up with about 80 integrity problems and went about correcting them. What I have found is that I have several queries all of which only display in rule form and when I change the attribute to the new value, and clear it from the display list for the query, I get an error that I am still referencing the deleted attribute, and I am quite certain I am not. I have about 12 of these and will probably recreate the queries but there seems to be something about this that is a problem.
To duplicate this, I recommend creating a query that will only display in rule form (I do not know the criteria for that) and reference some attribute - in my case I am using the attribute as part of the ORDER statement. Then delete the attribute and run integrity checking. Then when you get the error on the integrity check, go in and change the attribute. At this point, I am unable to save due to the integrity error which should be resolved.
If you can't duplicate this, I will send my BSV at your request.