Helen has been studying hard for the exam, so she should pass.
Can I put "will" in stead of "should" in this sentence? If so, is it natural and what's the difference between them?
"will" and "should" have different meanings.
Grammatically both are possible here, but "will" expresses greater confidence in the future outcome. "She will pass" = "I am certain", "She should pass" = "I expect her to pass, if everything else is fair."