When preparing artwork for printing, it is best not to select all objects and then flatten transparency because there is a risk that the .ai file would be saved in this state. You can Save a Copy and choose PDF as the format, and in the subsequent dialogue specify Acrobat 4 (PDF 1.3) compatibility. Then in the Advanced Section, specify 2400 ppi for the Line Art and Text resolution and 300 ppi for Gradient and Mesh resolution, with “Preserve Overprint” checked. BETTER YET, just Save a Copy as PDF, and then do all the flatten transparency steps within Acrobat Professional.