Hello I’m going to add to the discussion. Yes rendering each frame as an individual file. If you’re using individual render layers for later tweaking that can get a little crazy with the files. There is a file that was invented to cope with the problem you have naturally discovered:
OpenEXR
The good news is that it is already supported in Blender. I personally don’t know enough about it to teach you anything specifically. But that is the file format to use when creating animations and rendering each frame individually while preserving each individual render layer.
Good luck in your googlings.
