The 'it' refers to 'affidavit.' The sentence plays out like this: A prosecutor must ask a judge to seal an affidavit if (disclosure would jeopardize confidential informants), if it (would harm a continuing investigation) or if it (contained information from an unexpired court-ordered wiretap). In the main sentence the if is paired with affidavit. From that point on affidavit is substituted by 'it.' The sentence could be rewritten without the 'it' as: "A prosecutor must ask a judge to seal an affidavit if disclosure would jeopardize confidential informants, if the affidavit would harm a continuing investigation or if the affidavit contained information from an unexpired court-ordered wiretap." Would is a form of will. In the usage it means that there is a reasonable belief that not sealing the affidavit will result in what is listed. (jeapordize informants or harm an investigation)

All the 'it' words refer to the affidavit. In each case, you could use "disclosure of it..." The 'would' in the first instance indicates a potential outcome or effect, but in the second it is not appropriate, because the affidavit cannot 'would' contain something - it either does or does not contain information.

'it" its refer to the affidavit.... would=can