Some personal thoughts from me on that Jenny.
1. There isn't a publish list of these special attributes that I am aware of. Even the most careful and patient administrator is going to find it tough to know which ones are safe to change and which ones are not as the product doesn't prevent you from doing so. So if this the upgrade is going to continue to behave this way, can you see if you can publish a list of these attributes that need attention?
2. Product Management have previously confirmed that an upgrade should not change database mandatory properties when these have been set by legitimate use of the design tools. For example the change note title field can be changed using object designer to be non-database mandatory, so the upgrade should leave it that way. Why should it need to change it back really as there is no product functionality I'm aware of that needs it to be DB mandatory?
3. Errors like this can take a long time to work through for someone who doesn't have considerable historical knowledge of which attributes are special. If LD want upgrades to become smoother over time, I'd see this particular area as one that needs some thought.
Thanks for reading these musings and I'm very aware support cannot make the decisions suggested above, but hopefully they make sense and could be passed on.