Hi, unfortunately I haven't seen this bug report earlier. As upstream developer of pdfshuffler, I am against the proposed patch. It was actually an intentional decision not to include a save button. The reason is that the pypdf library is quite limited so that the pdfs processed with pdfshuffler may loose features (e.g. index) that are available in the original pdf. Forcing the user to go through save-as (initially it was actually called "export") gives the message that the output should probably be saved under a different name anyway.
Having a save button that silently replaces the original file with a file of inferior quality is a too aggressive behavior, not typical for free software. Hence, I do not plan to incorporate this patch in the upstream project and my recommendation to debian would also be to revert the patch. Sorry but it is a higher priority to protect user's data than satisfying user's commodity. Best regards Kostas