These are two separate options with no correlation.
You continue to make the monthly payment as specified in your contract. Failure to do so, for whatever reason, will mean the loss of the Jeep and greatly reduced ability to borrow for its replacement.
Its your Jeep and what you intend to do about the engine is your decision. There may be a warranty for manufacturer defects but that will not pay for repairs due to use or abuse. You decide if worth fixing and if so, who will do it- dealer or independent or yourself, and how you will pay for it. Might even sell it as-is with a blown engine or park it until you have the money and decide. No one can make that decision for you.
In my opinion, a $2-3,000 engine repair at a dealer is not indicative of a major issue.
But whatever you decide, you still owe on the loan.