so jetblue is running a 20% off sale today and im ready to purchase.

If look at DEN-RUT it says the discount is non applicable b/c of the cape air portion.

If i book DEN-BOS and BOS-RUT seperate using the 20% off i can save over $20 but then i have two itineraries and two one way tickets in reality. I am assuming this will make my luggage and transfer more difficult as i guarantee i will need to re-security check, re-check in and wait for my bags. Is this too risky a move for $20 in savings? It doesn't sound like jetblue will transfer it over unless its one itinerary i have two hours and its significant savings but if i missed my flight because of that id feel pretty stupid