Once you open a document with a schema it becomes memory resident. If you open another document with the same schema id but different schema structure (fields, documentation etc.) then this message occurs.
That would be the best case scenario the worst is when the issue becomes endemic within your Revit files or that of your clients. It becomes very difficult to fix if schema inconsistencies start to contaminate family files that then get added to project files (remembering that families can be nested).
It important to never change the schema once it has been created and is in the wild. You also have to bear in mind that a file may be upgraded and so a newer add-in with updated schema requirements should recognise the legacy schema and the updated one as two distinct schemas with two distinct ids (transferring over the information from legacy to new). If you keep the schema structure the same between versions then that is fine but I think this is rare because things evolve.
