The original sentence is
That hidden chambers were found by a stonemason while the house of worship was being renovated has not been revealed to the public.
That hidden chambers were found by a stonemason while the house of worship was being renovated - has a clause and the entire fragment acts as a noun. This is called
Noun clause and is considered always
Singular. X has not been revealed to the public - (Replace X by any noun) - This is grammatically correct.
Let's look at other choices.
A. That hidden chambers were found by a stonemason while the house of worship was being renovated has not been
This is correct.B.
Renovating the house of worship, hidden chambers found by a stonemason was not
Renovating modifies chambers - incorrectC. A stonemason found hidden
chambers renovating the house of worship but not being
Chambers renovating the house; Renovating modifies chambers - incorrectD. Hidden chambers were found while renovating the ancient house of
worship by a stonemason but
has not been
Misplaced modifier. Sounds the stonemason did the worship. "HAS" for chambers is incorrect. E. Renovating the house of worship, hidden chambers found by a stonemason but not
Renovating modifies chambers - incorrectHence , A is correct .