Amending returns can lower an IRS Subsititute filed return. If you has an audit that went poorly, you might be eligible for audit reconsidetion.
An offer in compromise doubt as to liability is made when there is a dispute as to whether or not you are really liable. These are actually quite rare as usually amending returns, or audit reconsideration works better. And in caseswhere youwill still owe something unaffordable, it might be more effective to file an Offer in Compromise doubt as to abiltiy to pay.
For liabilties causes by yourex or even current spouse, a 2011 tax court decision and agreement by the IRS now removes any time limitation filing an innocent spouse claim. In addition, there are other successful ways to deal with these issues using other, lesser-known approaches, including injured spouse and equitable relief.