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In the end I submitted a help request. It is possible to edit the XML file and modify/update the file links. First ensure that the option to compress the OO3 file is unticked/off - this is found in the document inspector and is set for each document and defaults to on. Next when changing the file link it is necessary to delete the alias="A56B....." portion.

Many thanks to April R. at Omni for the help.