After you've finished editing, just run it through qpdf without parameters, as explained in the beginning of the article, and it will recompress the data and recreate the xref table. No need for yet another tool.
I guess you could, but this is the source of the errors (actually warnings) that the article mentions. Probably best to fix the file with the provided tool (fix-qdf is distributed with qpdf) rather than get in the habit of ignoring warnings.
