The message that appears at the end of the calculation is to let you know that the gap is wider than the correlation equations provide for. But the program still does the calculation, and as the message says, it is probably correct.
In terms of generating the IDF file, I was able to generate the BSDF IDF file, which is what you would want for Energy Plus. Since Honey Bee runs Open Studio, which is basically Energy Plus, this should be what can be used for the input.
I generated the BSDF IDF file from the Glazing System detail view, and it was not empty (the standard IDF will generate an error saying it can't be written because Energy Plus does not support that shading model). I have attached the IDF file that I generated.
Robin