Four different answers

Only C is out of question.
On the second thought. I was completely wrong in my post above.
"Was decorated with artefacts" is not an action, it is a attribute of the cave ---> it means that past perfect and present perfect here do not pass.
(Thus A, C (anyway), D are out).
So our sentence has to sound something like:
"The man-made cave decorated with artifacts belonging to ancient Egypt's sea-faring vessels was discovered along the Red Sea during an unearthing expedition last year by the tean of arrchaeologists"
Now. Between B and E. I choose E.
Discovered along the Red Sea coast, the man-made cave that a team of archaeologists accidentally damaged during an unearthing expedition last year was decorated with artifacts belonging to ancient Egypt's sea-faring vesselsBecause "using artefacts" points on some action. It is like someone took an artefact (a stick for example) and used it (made a paint for example) to decorate a cave.
"with artefacts" means that someone took an artefact (an ancient stick, i do not know) and put in the cave - it makes much more sense.
Moreover, we can throw away th middle part of the sentence and all actions seem to be in their place - very good.
Discovered along the Red Sea coast, the man-made cave
that a team of archaeologists accidentally damaged during an unearthing expedition last year was decorated with artifacts belonging to ancient Egypt's sea-faring vessels
E---------------------------------------------
Discovered along the Red Sea coast, the man-made cave that
was accidentally damaged by a team of archaeologists during an unearthing expedition last year had been decorated using artifacts belonging to ancient Egypt's sea-faring vessels.
A. was accidentally damaged by a team of archaeologists during an unearthing expedition last year had been decorated using artifacts
B. was accidentally damaged by a team of archaeologists during an unearthing expedition last year was decorated using artifacts
C. accidentally damaged a team of archaeologists during an unearthing expedition had been decorated last year with artifacts
D. was accidentally damaged during an unearthing expedition done by a team of archaeologists last year has been decorated using artifacts
E. a team of archaeologists accidentally damaged during an unearthing expedition last year was decorated with artifacts