One of the sticky points in the controversies that surrounded Satchidanandendra was whether there is a root ignorance: Mullavidya even in self-realized persons (normally, Advaitins or followers of Shankaracharya). When Satchidanandendra (SSSS) and his former mentor, Krishnaswamy Iyer went to consult Virupakaksha Shastry (an authority on the tradition of AV) with that end in mind, the latter pretended to make them believe or accept that a remnant of Prarabdha Karma or Avidya always remains, even in jñani-s. After that encounter, SSSS and K. Iyer concluded after further reflection that ‘the Vyakdhyakaras (post-shankarites) were themselves the originators of that misconception’.
Subsequently, SSSS intensified his study of the Bhashyas for five years, during which time “he used to discuss and argue with reputed scholars with the intention of compiling a Sanskrit book called ‘Mullavidya Nirasa’ … which was finally published in 1929… there were hundreds of objections from every quarter… the battle of wits and attrition continued for the rest of his long life”.
An example of the above: a recent critic (Ramakrishnan Balasubramanian) has written: “No doubt SSS’s textual analysis skills are excellent, but the problem I see with SSS’s writings is his obsession with terminology, rather than philosophy”. The main criticism by the author, in respect of the interpretation of avidya by SSS, is that this is not due to a double superimposition of the self and the non-self, as the latter maintains, but only to a superimposition of a subject, non-self, on the self: “
The fundamental error is a superimposition of an observer on the real… and by a reverse process the inner self, which is the witness of everything, is superimposed on the inner-organ.
 Sri Satchidanandendra Saraswati Swamiji – By D.B. Gangolli, 1997
 Review of ‘A New Approach to Understanding Advaita as Taught by Sankara Bhagavadpada’ – by A. Martin –‘Advaita Vision’, 2014.