A subtle change, but a welcome one.
Copy-paste the code from the original enemy, then change the code to make it into a new enemy. This makes it separate from the modified enemy. Copy the base enemy's json and modify it. Change the values and stuff to the ones that your enemy uses, keeping any unchanged values from the original enemy intact. Change the name to match your graphic. DO NOT USE THE BASE ENEMY FILES FROM THIS MOD, USE THE ONES IN VANILLA. FOR THIS REASON, YOU SHOULD BACKUP YOUR MARI0 SE BEFORE INSTALLING THIS MOD.
This should make your custom enemy separate from the original enemy, which are modified. Hope this helps.