I have one of the windows
on my bench ready to take apart, so I pulled out one of the long screws from the bottom of the glass channel (I assume that this is the one you mean). It appears to be a #6 x 1.5" pan head machine screw, albeit a bit of a custom.
Most #6 machine screws are "6-32" which is a #6 screw with a fairly fine thread, that being 32 threads per inch. These are coarser than that by quite a bit, and unfortunately I don't have a thread pitch guage to determine exactly what they are.
I would be concerned that a 6-32 would be too fine to hold properly, but maybe it would be ok. The other alternative would be a #6 pan head wood/metal screw, but without actually trying it I am not sure. Size should be ok, and the threads are courser.
I did a bit of looking this morning, and can't see anything other than 6-32 being readily available. I will be curious to hear what others have to say, I have about 20 more of these screws to deal with, so breakage is always a possibility for me as well.
Over to others for input...