Can I connect the 3" flue to an existing 4" roof vent?
Without being on site to inspect the exact details of your application, I can not say for certain, whether your existing vent piping will work with the UDAP-45 unit heater. Your installer will need to confirm suitability and compliance with local and national building codes and regulations. Provided the above are met, you should be able to use your existing 4" venting.
Be aware that Modine requires that the vent pipe be made from galvanized steel or another suitable corrosion resistant material as condensation may occur in the vent pipe. With a larger vent, there will be more heat loss and a higher chance of condensation which can lead to corrosion and premature failure of your venting. You can find complete venting details beginning page 6 of the installation manual.