Normally when a construction loan funds money will be dispersed for the payoff of any existing leins (seller carryback) plus some money for the first stage of construction. So the seller carryback in and of itself won't affect your construction loan. Construction loans are pretty difficult to get in the current very conservative lending environment. I suggest you contact some lenders before you buy the lot to be comfortable you'll be able to do what you want once you own it. A carryback is a loan that you'll have to pay back and that means some form of payment. Since it is uncommon to be able to get any income from vacant land (like from renting it out as you could improved real estate) its more important to do your due diligence to be sure you don't get stuck with an alligator.
Call me and I'd be happy to discuss what you need to look for and what questions to ask a lender.
Your construction loan lender will want to be in first position at the time they lend you the money. So, they will require that the proceeds of the construction loan include enough funds to pay off the seller-carried financing (assuming the seller has recorded a lien, which they would be crazy not to have done so), and will require to do so as part of the funding/recording of their lien.
I am sorry, but there is no "eventually" or "maybe" to this situation. No construction lender is going to go into second position for even a second once they have lent you the money.
I certainly don't think that it would be a deal killer. Good luck on your dream home!
Korene L. Clopine-Seaman
Senior Mortgage Originator / Team Leader / Mortgage Lender
AZ License # LO-0916745
CA License # DOC-218520
Direct Phone: 623-340-0934