You can use conditional statements to check if a file exists:
import os
import arcpy
file = r"somepath\pdf.pdf"
if os.path.isfile(file): # exists - get a new name for the pdf
file = arcpy.CreateUniqueName(file)
The if state basically is saying if the file exists and the os.path.isfile() returns true, then call this ArcPy function that will create a unique name for your file.Also, to set overwrite output it should be:
arcpy.env.overwriteOutput = True # or 1