InDesign CS6 from CS3 plug-in issue?

Our InDesign CS3 files have the SBIndexPro plug-in that was required to generate an accurate index in InDesign CS3, which InDesign CS6 doesn't recognize because it's a third-party plug-in (and CS6 doesn't have it or require it). So if we open CS3 files in CS6, we get an error message that the SBIndexPro plugin is missing and book functions (exporting book to PDF, packaging the book, updating page numbering, generating TOC, generating an index) are all disabled because of it.
The work-around we've found from forums online is to open the files in InDesign CS3, export each file to an INX (InDesign Interchange) file, open the files in CS6 and fix elements in the master pages (running headers shifted and have to be moved back into place), relink any missing images, save as a CS6 InDesign file.
Is there any simpler way we can get our files updated from InDesign CS3 to CS6 without this plug-in tripping us up? We can see how to disable the plug-in in InDesign CS3 but the files still say they're missing the plug-in when opened in InDesign CS6.
A prompt response and any help is appreciated!

You could open it in CS6 and export it to IDML but besides that, you've
covered the only two ways I know.

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