You may want to move this question to the general user forum, this one is explicitly for scripting.
It's hard to tell what may be the cause, could be your "Include linked files" option when saving the document?
Where is the "Include linked files" option? When I do a File>Save it doesn't give me any options.
I'm not sure, if originally when you Save-As if the include linked files is off, if that would carry over into the simple "save". But how about this - when you imported the file, did you make sure that the Link box was checked in the file-open dialog?
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Thanks for the help. I turns out you only get the Save options when you initially create the file or if you do a File>Save As, not for a simple File>Save. When I created the files I forgot to uncheck the "Include Linked Files" checkbox. I did verify that the linked file remains linked when you close and open the host file if the "Include Linked Files" checkbox is unchecked.