"Where is the Welsh medium school?"
Translation:Ble mae'r ysgol cyfrwng Cymraeg?
Both seem to be used in the wild in the media and by schools themselves. It depends on how you parse the sentence. Ysgol cyfrwng Cymraeg seems more common and feels more correct..
Edit - I cannot find ysgol cyfrwng Gymraeg anywhere on the course database - where did you see it?
OK, thanks. Yes, the different types of words in the two phrases make all the difference!
In ysgol cyfrwng Cymraeg, Cymraeg is an adjective (Welsh, Welsh-language) describing the noun cyfrwng (a medium). Since cyfrwng is masculine there is no mutation of Cymraeg.
In ysgol gynradd Gymraeg both cynradd (primary) and Cymraeg are adjectives describing the feminine word ysgol, so both must mutate.