Got any pics?..its hard to guess what it might be.
Hard things to remove:
tar spots ,tree sap,bird dirt whichich is a bit acidic and has lime and egging,especially if its been left any length of time.
Get at the glass first. work your way up thru liquids to see what might clean it .
thin window cleaner/vinegar applied with a newspaper,petrol,white spirits,etc.
If none of those things clean the glass and its still "stained" it must have been something very powerfull
The paint..I dont know.. see how you do on the glass,it depends on what takes the coating off the glass.
acids ,even hi concentration strong ones are stored in glass containers.
If whaterver was thrown on is actually strong enough to "cut" glass, Id think your paint would have peeled down to bare metal .
post a pic or 2 see how commonly available solvents do on the glass(dont splash it on the bodywork) and wait for a reply from S.M.A.R.T. Paul, aka the bodyman