'Work' is usually an uncountable noun and therefore used with the singular form of the verb. So you could say 'I was relieved when all the work was done or had been done. Both are correct. We can use both the past simple and the past perfect to refer to an action which occurs before another in the past. First the work was done then I was relieved. First the work had been done then I was relieved. Works in the plural refers to a) roads, bridges dams etc ex: Engineering works b) a place where industrial labour is done ex: Steelworks. c) the moving parts of a machine. d) works of art e) an informal way to say everything. 'I want a pizza with all the works' = with all the toppings.

I was relieved after all works were done/all works had been done? None of these are correct. You probably mean "work". I felt relieved after all the work was done. I felt relieved after all that work had been done. Both of these can be used.

I think it is the second one.