The obvious path: Open the .map source file in a programmer's editor, search for the coordinates, take note of the brush number, then search for that brush number in GTKradiant, delete it, to then recreate it... alas, does not work. Because those coordinates for some reason are not in the .map file.
@Silicone_Milk
I have not noticed it, yet. But that may only mean I have not been looking closely enough.
@Delirium
Alas that link is about terrain. Though it does hint that massive amounts of not properly caulked brushwork (here terrain), may cause such an issue. I have been "relatively" on the ball concerning caulking, though.
Make a new level and copy paste over the old level? That has solved similar errors for me when I have had brushes that for some reason didn't exist but actually did existed...
You have a surface where two or more tris (triangles) share the exact same coordinates. It doesn't really matter, though. q3map2 simply filters out the duplicates.
Hmm... my changes to the geometry in the map, adding new areas, I almost completely deleted one sector seems to have removed the issue... whee... I think.
I was a tad slow to "get it". I could have located the location in GTKradiant, using those conflicting coordinates, to delete the brushes there. Still strange that the exact coordinates (i.e. vertices) are not in the map file, q3map2 may be referring to a plane instead.
Yeah, they're coordinates on the same surface (as in brush face). The warning occurs during the meta phase, when surfaces are merged, so if you have any intersecting brushes, that might well be the cause.