Married Couple owning a Duplex living in 1 unit renting out the other unit. Filing separately this year

[jlzinck]

Here is a new one for me. I do taxes for friends and am at the point where I am about to tell them to go to a CPA/Tax Accountant.
Couple is still legally married but have lived apart for a few years. They have always filed jointly because it has been easier and more beneficial to them.
This year they are filing separately. 
As one of the couple lives in 1 side of the duplex and they rent out the other they have always used 50% of the deductions for business and the other 50% for personal.

Were they to agree that the owner living in the duplex take all the income and deductions on their return would this cause an issue as they are both listed as the owners on the paperwork and have filed jointly the past 20+ years?

Just wondering the best course for them.

thanks 

[MaryK4]

No, there would not be an issue for one spouse to claim the income and deductions for the rental on a separate return.  As long as all the income is reported, as a married couple there is no problem with how they divide this (unless they are in a community property situation).

[jlzinck]

Thank you very much