When Ghostscript reads the main PDF generated by the TEX system with embedded PDF files and outputs the final PDF, the PDF page mode and name targets etc. are not preserved. Therefore, when you open the final PDF, it is not displayed correctly. Also, remote PDF links do not work correctly.
This program is able to extract the page mode and named targets as PDFmark from PDF. In this way, you can obtain embedded PDF files that have kept this information.