Ask the USDA ... that is a program that very few people are knowledgeable about.

Looking at the program:
Applicants must:

• Meet income-eligibility
• Agree to personally occupy the dwelling as their primary residence

I don't know how long you have to have the existing dwelling as a primary residence.
It says applicants with questions should contact an approved lender.

All the best info is on Rd.usda.gov. That is the official site for USDA loans and has the handbooks for lenders as well as applicants.

you are agreeing to occupy the house as your primary residence so I believe there might be a issue when you finish the second home.

or possibly that line item "agree to personally occupy the dwelling as their primary residence" is meant to prevent using this as rental property - just ask someone who is knowledgeable (make certain they really are).

The UDSA office personnel are very nice and willing to work with the public, not so much lenders. Call your local office and ask your questions. I had to call the state director myself when closing our loan.