The document is in failure mode: an operation has failed, and Revit requires the user to either cancel the operation or fix the problem (usually by deleting certain elements). -or- The document is being loaded, or is in the midst of another sensitive process.
The Schema remains in memory. Any schema the schema is a sub-schema for will not be impacted. All data referenced by the schema as the result of being a sub-schema will remain in the document.