This questions tests your knowledge about Verbs, modifiers and tenses. Let us deal with it by taking one option at a time.
Metallurgy, the process of refining metals from naturally mined ores,
as a method of the moulding of metals, it was well known as early as the medieval period, but until
about several decades ago workers did not realize that bacteria take an active part in the process.
(A) as a method of the moulding of metals, it was well known
This is a classic case of repeating a subject.
The sentence reads something like this:
Metallurgy, ... , ..., "it" was
Watch out for this error in sentences with long modifiers.
(B) as a method of the moulding of metals well known
This option changes the meaning and incorrectly suggests that metals were well known.
Also, it lacks a verb too.
(C) was a well known method of metal moulding
Correct
(D) was a well known method of moulding metal that was
This option changes the meaning and incorrectly suggests that metals were well known
(E) had been a method of metal moulding, well known
Incorrect reference of well known. Here well known is pointing towards the metals and not the process.