What is the function of the waveguide flanges?

Hi lord

It simple. just to connect between two waveguides.
you can't use one piece when you bend it you have to cut the WG
then you connect the pieces with flanges or brazing.

PL

The flanges are also milled to have a half wave path to a short so that the gap across the two halves looks like a solid piece of metal and does not affect the waves going down the guide.

What you are describing is a "choke" joint, and only high power waveguides use those (to stop current arcing at the flanges).

Most people just use flat "butt" flanges for both sides of a junction.

Speaking of high power, I once worked on a RADAR that had such high power that the waveguide was pressurized with a special gas (I vaguely remember that it was Sulfur Hexafluoride) to increase the voltage breakdown. Then the signal was specially modulated for pulse compression with an over 1000 compression factor.