In general, the pdfwrite file does not know that you are adding files, so it saves bookmarks and other metadata data on the assumption that you want them in the output.
However, when you merge PDF files, saving information will not work, because the page numbers for the second and subsequent files will be incorrect.
So, you need an approach with two passes, first merge all the files, drop the bookmarks, then "convert" the combined file and add pdfmarks to set the correct bookmarks.
There is currently no option (with pdfwrite) to not save bookmarks. To do this, you will need to modify the PostScript files for the Ghostscript PDF interpreter. You can try setting -dDOPDFMARKS = false, but I doubt it will work.
Kens
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