I can't believe that Spectra doesn't have its ISEs. The BS001 was supposed to remain in France until it had its ISEs and be delivered with its ISEs, and then the ISEs were supposed to be deployed on all the other Rafales already delivered. If that hadn't happened, it would have been a scandal and Dassault would have had to pay penalties. India does not hesitate to apply penalties when they are due, and sometimes even applies them wrongly, as in the case of MDBA, where it applied penalties believing that the MDBA contract had been signed at the same time as the Rafale contract. So your story seems very dubious to me.
What's more, the Rafale has no problem approaching SAMs in terrain following mode and should be hidden in the ground clutter for SAAB's AWACS due to its distance and Spectra, so something went wrong.