I agree that the context of 2:62 is the story of the people of Moses (pbuh) but the fact that 2:62 includes the Christians and the Sabeans, without specifying an era, tells me that the verse is making a general moral out of a specific story, and therefore cannot be said to apply to specific times.
The dilemma to resolve, if there is one, is that people cannot be "among the losers" and "will not grieve" at the same time, so the people referenced in 2:62 must not be the people referenced in 3:85. How can that be? The only way I see how is to notice the particular verb God uses in 3:85, يبتغ
which means to seek or to desire. I do not, however, quite know its significance. Ibn Katheer, rahimahullah, says that it means preferring his religion even after God has sent a new prophet, e.g., Jews staying with Judaism and not accepting Jesus, peace be upon him.
BTW, Abu-Abdillah Shu`la, in his book صفوة الراسخ في علم المنسوخ والناسخ, page 98, includes this verse in this abrogation claim which he rejects:
Shu`la's refutation is that all three verses can be easily combined
. He said that if God had said in 2:62 or 5:69 that the named people's religions were accepted, then the claim of abrogation would've had merit. But, Shu`la noted, God clearly qualified those people by saying that they believed in God and the Hereafter and that "cannot be without believing in Muhammad (PBUH)."
I think what he meant that people who have not heard of Prophet Muhammad (PBUH) and his message but believed correctly are the ones covered by 2:62 and 5:69.
Anyway, it is good to see that he believed that as long as there is an explanation that makes the abrogation claim unnecessary, such claim should be rejected.