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Have you recently added the external DTD rule or moved the documents you are exporting to a different directory? Unless the API client is changing the external identifier (Scott?), FM does not merely copy the system identifier in the external DTD rule, but tries to interpret it as a relative filename and generate the corresponding absolute path. As you have seen, this attempt is not always what you want.
--Lynne
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You write that:
But the xml fails validation tests outside of Frame. The result reads: Line: 9; Line Position 3; File Position: 212; Error: The system cannot locate the object specified. Error processing resource 'ditabase.dtd'.
You'll either need to replace the relative pathname produced by FrameMaker or provide an appropriate search path to your other XML tools so that they can find the DTD.
--Lynne
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Do you have a backup of a configuration that worked? If so, you might compare it, one file at a time, to the current system. Have you updated FrameMaker itself in the meantime?
--Lynne
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