Do Freddie Mac or Fannie Mae accept a mortgage refi with a home that has a Mother in law suite?

this is still considered a SFR, there is no change in qualifying

Generally it is considered a mother in law and there is no difference from a standard Single Family Home in how they view the property, however, you would make sure it is not classified as a two unit or it simple would mean a more costly refinance in rate or expenditure for the same rate.

This should present no problem. We would love to do this mortgage refi for you. My number is 301 915 5644 and you can reach me any time. Thanks

It depends whether it conforms to local building and zoning codes and if it is typical for the properties nearby.No lender wants a property that is outside code or unusual unless justified

As others have said, that is still a standard mortgage. The bigger question is if the appraiser can find good comparable sales to reach the needed value.