I think this relates back to a general question about classical Indian tunings and probably the history of the 22 śruti system, well known from ancient texts like the Nāṭya Śāstra. The problem with many of these references in ancient texts is that the exact tunings aren't given or are given in vague terms, leading to the many different proposed systems (see the link above on śrutis).
Whether any of the proposed systems are the "correct" ones and equivalent to ancient Nāṭya Śāstra tunings is a matter for debate. It is true that as equal temperament has spread around the world through European colonialism and in recent decades through global pop music, many traditional tuning systems are being undermined and perhaps lost completely.
On the other hand, there is also a question in Indian music theory similar to one that plagues the history of Western music theory concerning how accurate historical tuning systems were. In ancient Greek music theory, this is often framed as a debate between the followers of Pythagoras (for whom exact mathematical ratios were paramount) vs. the followers of Aristoxenus (who seemed to take more of a view that one should tune notes where they sound good, using practical approximations). The inexactness with which ancient Indian texts are sometimes associated may be due to the fact that practical musicians in most places throughout history likely spent more time actually tuning instruments to what sounded good to them (and what was commonly practiced around them), rather than doing mathematical tuning calculations and measuring out ratios on strings.
To relate this back to the question, it's thus very likely that some methods of tuning have been lost to time, as they were likely local or regional scales that just "sounded good," and no one ever bothered to see how they might correspond to mathematical ratios and thus write them down in a way that we could replicate today. As teachers and students in some traditions died out or migrated and took up different regional customs, these ways of tuning may have been lost. As the article linked above on śrutis notes, actual analysis of performance of Indian music reveals that tuning systems vary from performer to performer, from piece to piece, and sometimes even within the same raga, suggesting that there may never have been a sense of "one true" scale tuned according to some system of ratios or whatever.
In fact, quite a few scholars have suggested that Indian music theory has actually also been "colonialized" by Europe in the sense that attempts are now made to fit traditional Indian music to just intonation scales and ratios (something European theory has been obsessed with) that perhaps weren't very relevant to ancient Indian texts. (I believe the earliest clear references to string length ratios in measuring intervals in Indian theory date to the 17th century, and even then, they are not used to define complex tuning systems.)
Modern Indian attempts at systematization of intervals may have more in common with modern European theory than with actual ancient scales. European interests may thus be both partly responsible for spreading 12-TET and for creating an obsession over some "lost tuning system" that may never have existed.
(See, for example, this article which describes the spread of the harmonium with its 12-note tempered chromatic scale being perceived in India as being in conflict with traditional tuning. But the article also describes the rise of European and Indian investigations into measuring scales in the late 19th century and early 20th century that were meant to simultaneously quantify the supposed just intonation scales of India, while explicitly creating a distinction between such scale systems and European 12-TET.)
alternative-tuningstag because I'm asking about historical tunings that predate the equal-tempered scale rather than "alternatives" to it.