The period when the great painted caves at Lascaux and Altamira were occupied by Upper Paleolithic people has been established by carbon-14 dating, but what is much more difficult to determine are the reason for their decoration, the use to which primitive people put the caves, and the meaning of the magnificently depicted animals.
(A) has been established by carbon-14 dating, but what is much more difficult to determine are
(B) has been established by carbon-14 dating, but what is much more difficult to determine is
(C) have been established by carbon-14 dating, but what is much more difficult to determine is
(D) have been established by carbon-14 dating, but what is much more difficult to determine are
(E) are established by carbon-14 dating, but that which is much more difficult to determine is

Here correct ans is (B). But isn't saying "what is" wrong due to the compund subject created at the end by "and". This is a typical case of "Flip it" (SC guide). The subject comes after the verb and would require a plural verb "are".

This is an obscure one! I'll do my best...

The OG says that "what is much more difficult to determine" is the singular subject of the second independent clause. If that's so, we should be able to substitute "the thing (that is much more difficult to determine)". Viewing it that way, the sentence reads:

"....the thing (that is much more difficult to determine) is the reason..., the use..., and the meaning..."

The singular "is" is correct because it has to match the singular subject "the thing" NOT the plural object "the reason, the use, and the meaning." It's Subject-Verb agreement, not Object-Verb agreement, that we require.

The flip doesn't work here because the sentence is already in Subject-Verb-Object order; by flipping, we would erroneously be switching the plural object and the singular subject, changing the verb that is required!