That is a fourth and entirely new meaning to "flatten" for us. A plug-in could in theory be written to do this but in the general case working out what elemens are completely hidden by overlap would be very hard. Also, if there is transparency, the hidden elements may participate in colour blending. Very detailed knowledge of 32000-1 and hidden object removal techniques would be needed. Not a task I would undertake!
I think you may be going off on the wrong track. You have a colour problem, and you decide you want to remove hidden elements (which will only affect colour if there is transparency). I would go back to the ORIGINAL problem. Maybe it's your colour settings in printing.
But I should note that converting PDF -> PS -> PDF is officially discouraged as it is considered a poor workflow.