Pay for 2 hours consultation time from an attorney experienced in contractor real property law (if you don’t know of an attorney contact me and I will provide a referral) to understand the specific applicable laws, the risks, and potential costs2.

The right lender will be able to advise you on what options you have after getting some info from you and taking an application. 

In some cases, exemptions or adjustments might apply for buyouts between co-owners, so it’s best to check directly with a local real estate attorney or tax advisor to confirm the exact tax amount and any applicable exemptions.

The standard to apply is quite simple: Did you accurately disclose the character of the down payment funds to the lender in the loan application?

Google search gives me these super wide ranges and mostly talking about adding a bedroom in a SFH, which I'm not sure if applicable to this situation of "moving/subtracting a bedroom from one unit and add it to another unit in a duplex". 

Quote from @Emily Mohr: Software is a common question on BiggerPockets.

If you prefer a software, we can discuss that.That being said, if you're interested in hiring an REI-savvy bookkeeper, I'm happy to introduce you to a few candidates so you can interview them.If you're interested in continuing to be your own bookkeeper, I suggest joining the FB group I mentioned so you can get your questions answered as you're working through your books.Also, I'm happy to help if/when you have specific questions.

Software is a common question on BiggerPockets.

it's probably just a matter of casting a wider net in terms of applications. 

In most cases, they learn of the transaction only when a Certificate of Occupancy (CO) application or a permit is submitted for repairs or inspections. 3.