Hi,
Finally, the PDFs are to be printed to a physical printer (=> physical pieces of paper) and also to be provided to the third party like digital documents. The result should not have layers switchable to on/off, but I believe this can be handled by printing the final (even layered) PDF to another PDF by a virtual printer (e.g. pdfCreator).
Layering was only an idea, which - as I believed - should lead to the goal; although that would probably mean to print the (layered) PDFs manually to the virtual PDF printer.
Or is there another (non-layering or layer-merging) way?
if you want to get rid of some part of PDF documents and if they are not too many, you can try to import them in Inkscape editor and really delete what is unwanted. Regards Zdeněk