I'm responding cos no one else has but Im probably not best placed to help.
Can you confirm both files are actually .wsdl's rather than say 1 .wsdl and 1. xsd? I don't mean by checking just the file extension here - I mean check the content to see if 1 is actually a schema (.xsd) rather than a second .wsdl?
I'm unsure why exporting the SOAP Service would generate 2 .wsdls. I do know however, that .wsdls either import the associated schema or embed that detail within the .wsdl content itself, hence the reason why I'm wondering if the second file is actually a schema file instead....??
If that's the case, you can edit the file to replace the import schema option with the embed schema option - but SoapUI doesn't do this as far as I can tell - you'd have to edit the file manually yourself.
if this helped answer the post, could you please mark it as 'solved'? Also if you consider whether the title of your post is relevant? Perhaps if the post is solved, it might make sense to update the Subject header field of the post to something more descriptive? This will help people when searching for problems. Ta