Engine Funny Noise problems of the 2014 Hyundai Elantra

Dec of 2017 the car stalled while I was driving through a tunnel. Luckily we weren't moving really due to traffic. The car started right up and was fine. Jan 2018 my engine started to make a loud thumping sound, especially upon cold start up. Brought vechile in Feb 2018 bc the souls was starting to happen all the time. First trip into Hyundai they told me there were no codes coming up and it t was bc of my oil filter not being be correct size. However, I have had my oil changes done every 3-5 thousand miles and never once had any issue, ever. Mind you my car just turned three. They changed the oil filter even though I literally had an oil change about two weeks earlier and the issues starts in December. Nothing changed and nothing was fixed, the sound was still there. Brought it back about a week and a half later overnight so they could do the cold startup. Hyundai called me that morning and said my engine was failing and that I needed a new one replaced. I waited three months for the replacement engine bc it was on back order nationwide. I relieved the car back mid may on a Saturday. That following Monday the car was dead. Could not start it. The car was towed to Hyundai, and the battery was dead. Hyundai replaced the battery. About two weeks later I started having issues while idling and in gear. The engine was skating and my rpms were going over 1 just sitting. I brought the car in and they again told me there were no codes and that the engine needed to get used to the car again. Another two weeks go by and now it's getting worse and it's especially bad in reverser. I brought it back in and they said that I needed my ignition coil packs changed bc my engine is misfiring. They sent me home with my car and said it was fine to drive. A few days later I leave work and it won't start again. It was towed to Hyundai and they can't find anything wrong.