What I have done is remove the Unique ID from the "Replaces Thing ID". Then set he Unique ID of the old one to be *HIDDEN. I then update the Name of Thing and Text to explain what should be added to the character to fix the issue.
So lets say I had fS2Dodge that replaced "fDodge" a feat in Pathfinder. I would remove the "fDodge" from replace thing id. Then on the *HIDDEN tab I would add "fS2Dodge". This allows a .por to load without errors but it will still show this now HIDDEN thing and will highlight it in red. It will give a nice message about this is feat no longer working.
I then change the name from "Dodge" to "Remove this add Add Dodge". In the text desc I may put "This is now depreciated and no longer works. Please remove it and re-add the new DODGE feat to your character".
The gamer is now given helpful instructions on how to fix the issue and not cryptic errors about "Missing Thing in Batch XXX".
