You don't want to remove the

boot.scr

file from the eMMC, just the one from the NVMe. You also shouldn't need to reflash the eMMC since that should have a fresh OS on it already from your last reflash attempts. It's just that the bootloader on eMMC is configured to check NVMe first and, if it finds a

boot.scr

there, it "changes its mind" and switches to booting from NVMe instead.