In the variant configuration scenario, there can be instances to discontinue a characteristics from the Class.
So people generally remove them from the class.
During the removal system generally provides a warning message and we over ride the same.
In such case if they are already used in the sales order, there are chances for creating the inconsistency in the sales order configuration( VC).
When we face such situations in the configuration we will be seeing the inconsistency icon as below. The red color x mark indicates the inconsistency.
Note: In case if this was helpful or if there is a better approach for this problem do write a comment.