Right so I did an experiment as well and it went like this.

Created a new folder and added one linked schema -> export went OK including the linked schema
Added a query based on the linked schema -> got the error.

Please note the query is valid.

Please see attached the labkey error file.

The log shows a null pointer:
Error creating linked schema test_linked_schema
java.lang.NullPointerException
    at org.labkey.query.LinkedSchema$LinkedSchemaUserWrapper.<init>(LinkedSchema.java:452)

And then the error that gets displayed on screen:
Unexpected server error
java.lang.IllegalStateException: Could not find schema test_linked_schema in /Genomics England/ext_sch_test for user null with query test_linked_schema_temp_214
    at org.labkey.query.QueryDefinitionImpl.getSchema(QueryDefinitionImpl.java:412)