I am sitting with the same problem. Seven years later! I have two Illustrator files with hundreds of the same size artboards which need to be merged into 1 file. May I ask, for what reason are your files not PDF compatible? (Hoping to learn something here) What about opening the files to be merged in Illustrator, then saving each file as a PDF compatible version? Then opening in Adobe Acrobat to merge? Have you tried that or would exporting as a compatible versions not be possible?
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