I had a very quick look at fares from India to the USA in business.
Taking BOM as origin and IAD as destination, the fare for one pax is between U$5000 for 'Special' and U$8500 for 'Flex+'. The difference between "sepcial' and 'saver' is only U$700 each.
So it is conceivable that when the TA was asked for a quote including CD and lounge access, only Flex+ was available. For two pax that would be a difference of U$6500 or thereabouts. On the previous occasion, the OP's parents may well have had a 'saver' ticket, which explains the entire story.
Generally, when a TA is asked to book a ticket, they offer the 'best' fare available. And (unless they are really careful and understand the nuances of EK fares), they might not see, let alone communicate what you miss with the 'Special' fare class ('H' bucket).
I think the solution (Marhaba plus private transfers) is very good.