Ongoing and unexplained RDS

My baby was flown to a level IV NICU when he was 1 week old. We took him to our local ER for very rapid breathing (90 breaths per minute) and retractions. Come to find out our poor boy had sepsis, Cardiomyopathy, a PDA, small aortic valve, a VSD, and fluid around his lungs and heart. The sepsis has resolved, and most of his heart issues have also resolved except for the small VSD. He doesn’t have any fluid around his heart or lungs anymore either. This is all great, however it has been 3 weeks in the NICU and he is still requiring 1L oxygen flow to breathe and even at that still has periods of respiratory distress. He isn’t requiring any extra oxygen he is on 21% which is “room air”, but just seems to require the flow. Doctors seem to be stumped about what is still causing this. I was wondering if anyone has a similar story.