Thanks Holger - 

OK - I saved the imported ontology like you said. 
Inspecting the contents, I find the only difference from what I got by 
downloading the TTL file directly from W3C was the insertion of 

# baseURI: http://www.w3.org/ns/locn

This is a comment! http://www.w3.org/TR/turtle/#sec-grammar-comments 
But I guess it is important to TopBraid. 
I've previously noticed similar comments used to indicate imports as well. 
Hmmm. Now we are getting into (black) magic? 

Furthermore, when I put a copy of this saved file in a place where I could 
open it, then TopBraid automatically created a second Ontology resource 
whose URI is the baseURI, in addition to the explicit one already in the 
file. 
So clearly TopBraid insists on having an Ontology present whose URI is the 
baseURI declared in the file (graph). 
If you make any changes to the file and then save it, you end up with two 
ontologies in the file, which in turn confuses some other tools. 

One of my colleagues has pointed out that this may be coming from OWLAPI 

"the automatic ontology IRI mapping tools in OWLAPI assume that the base 
URI is the ontology IRI.  As far as I know this should be just a 
convention."

Is this the source of the problem in TB? 

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