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I wasn't having any problems getting the file path information, I could toss it into a display dialog and see that it was there.

With much thanks to Paul, one of the Support Humans, and the unnamed engineer he got info from, my script is working again.

It required avery minimal change. I had the following two lines:

save first document in pdfFile
save first document in jpgFile

and the change that made it work is

save first document in file pdfFile
save first document in file jpgFile

where pdfFile and jpgFile are the full POSIX path/file name info

Apparently the comment on the upgrade page from Apple about not using strings to save into just means you have to specify that it's a file.

Also, he said that if you move your scripts from ~Library/Scripts to ~/Library/Application Scripts/com.omnigroup.omnigraffle6 (you’ll have to create the folder) you have the added benefit that not only should it work everywhere in the file system that you can edit your toolbar in OmniGraffle and add the scripts right into the toolbar. I haven't tried it yet, but that sounds handy.