An important article on Frithjof Schuon has just been published in Numen 64 (2017), pp. 258–293: This is Gregory A. Lipton, "De-Semitizing Ibn ʿArabī: Aryanism and the Schuonian Discourse of Religious Authenticity."
Lipton starts by noting the importance of Schuon for contemporary understandings of Ibn Arabi and commenting on the "posthumous Schuonian renaissance." He then goes on to make two arguments:
Firstly, he demonstrates by numerous citations from Schuon's works that Schuon subscribed to understandings of race and of the opposition between Aryan and Semite that were developed in the nineteenth century by theorists such as Ernest Renan and Joseph Arthur de Gobineau, and incidentally underpinned Nazi racial theory--I say "incidentally" because Lipton is not arguing that Schuon was a Nazi, merely that he subscribed to understandings that the Nazis also subscribed to.
Secondly, he shows that Schuon disliked what he saw as Semitic in Ibn Arabi, preferring Vedanta and Plato as Aryan. He was sometimes very critical of Ibn Arabi, for example for his “abrupt and unintelligible denominationalism.” Lipton understands Schuon's and the Maryamiyya's turn away from its originally very Islamic Sufism to a more universal understanding that de-emphasized Islam and instead emphasized the Virgin and Vedanta as a response to this problem, as "de-Semitizing."
The article is clearly written, tightly argued, and entirely convincing. There may also, however, have been other reasons for Schuon's turn away from Islam.