This is going to be a long list but I’ll need some time to assemble it. Bear with me!
Placed PDF files disappear on the exported PDF: try putting the disappearing PDFs on a separate layer underneath all other content. The full story is here.
Thin white lines on screen and output
Sometimes thin white lines appear which are 0 point strokes that are turned on and that will be printed because some RIPs and preflight will make them big enough to print if you set it up that way. If you triple click one of the elements in Acrobat Pro it will select all of them and then if you un-check the stroke box in Pitstop it will get rid of the lines.You can also run a fixup preflight in Acrobat that will fix them or use a PitStop action.