Yeah you will almost certainly need to download the chain from scratch. If you want to attempt this you would need to stop lightning during the process. Remove knots, install core and then let it sync. Once it’s fully synced you can start LN again. Might be worth checking with Start9 team if there is a way to do this since you may even have trouble removing knots without removing LN since it’s technically a dependency. Hard to say for sure without giving it a try.