Disappearing elements in a pdf when flattening

I suspect that this has been discussed before, but we put together a publication, and receive PDF ads from many sources, so I don't know how they are built. Sometimes, if we either flatten the PDF, or open it in Photoshop, elements will disappear. Sometimes just a portion of a logo will disappear, and if we don't notice it, the publication ends up having to refund the client. Any ideas what's causing this and how to avoid it?

If you rasterize or open a PDF in Photoshop you will see not only a small amount of loss of quality, it will be huge:
Vectors and fonts are rasterized with the image resolution (e.g. 300ppi). That means that theit lines are not crispy any more. If they remain in vectors they will be later rasterized in the RIP or APPE which will create much smoother lines and output in higher quality.
A PDF can contain a lot of different color spaces in RGB and CMYK. Photoshop will open a PDF and convert it to a single color space.
A PDF might contain transparency, saving as JPG will eliminate and flatten any transparency.
It would be much better to set up a standard how your clients should deliver their adds like
PDF/X-4 (which will include all used fonts embedded, not allow interactive objects, etc.)
Bleed
Output intent
Minimum resolution of images
Minimum width of lines and small letters
Minimum width of lines and small letters, when printed on black and also when printed on 4c.
If you need registration marks.
These things I am always asking for BEFORE I start a project. This will help to avoid errors and problems from the beginning.
Opening a PDF (nor a delivered EPS) is not a solution.
Sending the Add as EPS is neither a solution.
Sending a rasterized anything is also not a good idea.

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