From the above description, I do not quite see what the problem actually is. Is there any issue with having "-3A" being a part of some URI? Why is this ill-formed?

We do of course have some degrees of freedom when building these URIs, but the reserved character # has some technical ramifications that are not desirable: The above will create URIs such as

http://biomedgt.org/index.php?title=Special:URIResolver/Property#Testproperty

which tries to use "Special:URIResolver/Property#Testproperty" as a parameter "title". But # cannot be part of a URL since it marks a URL-Ref, so in the above the parameter title is assigned "Special:URIResolver/Property" while "Testproperty" is a references applied to the whole URL. So it seems to be better to use some symbols without special relevance to the URL-spec. This is exactly what "-3A" was meant to be (it is an "escape" of the URL-colon %3A, and follows SMW's general escape strategy for problematic symbols in URIs).

Anyway, Denny (currently maintaining the export) should have a look at this.

I close that now since there was no further detail provided on why this should be a problem. We have tried SMW's OWL/RDF with many tools, and most did not have problems (and none had problems with the -3A).