If elements disappear from the PDF after uploading to E-pages it may be because of the use of layers and layers with transparency in the PDF.
PDF versions later than 1.4 introduced the possibility to make transparency and more layers.
Unfortunately this can be interpreted differently on different PDF tools like rendering and rasterisation programs which is why printing houses prefer receiving the material in a single layer.
By using flattening you get only one layer, which is more easy to work with.
You can flatten the PDF in two ways:
1. Print to postscript and use Acrobat Distiller to make a PDF afterwards. The PDF version is not important - the postscript process will flatten the PDF.
2. From Acrobat Pro you can flatten layers by saving the PDF as an Optimized PDF. Pick "Files" -> "Save as" -> "Optimized PDF". Check "Transparency" (See screenshot below) and press "Save"
It is a well known problem in the graphical industry to handle PDF files with layers and transparency which is why Adobe and others have written some recommendations about this subject.
See examples here: