Instead of using the multiply blend mode, why not change the opacity of the layer? You could then render to a codec that supports an alpha channel.
What is your intended future use of this clip?
I work in video games, so I need this to be a flipbook which is essentially is a higher res gif image. I need all the frames as pngs. Opacity looks really muddy and doesn't work correct, why would they have blend modes if you could do it with opacity?
just to clarify I know how to render out to png, I just need a way to get blending to look right. I was thinking about using the layer as a luma for black and just having duplicate so only parts of the black show where the particles are coming out. Not sure if this is best way to do it though?
I'm having trouble picturing what you're trying to accomplish. Some stills or an example video might help.
There is no way to have blend modes be in a finished file. PNGs do not support blend modes, so we will have to achieve what you're trying to do in some other way.