If elements disappear from the PDF after uploading to LIVEdition it may be because of the use of layers and layers with transparency in the PDF.
PDF versions later than 1.3 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 three 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. If you will export from InDesign and use flattening you need to export it as a PDF 1.3. With a version 1.4 or newer versions there will be a risk that the files keep the layers if there are any.
3. 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: