Has any work been done to tear down walls and make this one unit?  I've had clients who have done that.  Once they started having kids, rather than move to a new house with more bedrooms, they just expanded their dwelling unit to include the rest of the duplex.  Obviously that depends on the physical situation.

I'm not sure if it's relevant but has anything been filed with the city/county to merge the dwelling units?  Around here Zoning would have to get involved at some point to legally "merge" two residences.  YMMV.

As Bill mentioned, you're not going to have a full exclusion in any case.  You'll have gain to the extent of depreciation AND prorated gain based on the Nonqualified use from 2009-2019.  I haven't had to do that math in a while so I'd have to look it up.

Were the rental losses allowed or limited?  I can't imagine you'd go from full 2/3 rental to only collecting half the rent but still reporting all of the expenses and have net income.  If there's no change to the bottom line on the tax returns from 2019-2021 I might be inclined to just refigure the carryovers and keep that documentation on file.  Then use the correct information moving forward.  You could include a preparer note with the 2022 return but I don't know that you'd need to if the tax did not change any.  If it does change taxable income I would likely disengage if they don't choose to amend.  Life's too short.

Rick