@Jacques Lucke (JacquesLucke) Hey sorry for replying so late, The problem that i am experiencing is that I wanted to do I water simulation with the new Mantaflow simulator, as I saw that it can add particles like foam, when I tried to bake those particles, spray and bubble particles too, I saw that all the particle systems are exactly the same, as I switched them on and off to see if they were different, if you try to switch the "viewport display" option on and off, you will see that all system look the same.

Also weirdly I cannot open my blender file anymore, even with the same blender version I was able to open it before

Same here. Baked a simulation, added all 3 particle types and baked them as well. The 3 generated particle systems on the object contain exactly the same particles.
Simple .blend is provided - rebake necessary of course. (Also, I have the feeling that
a) the initial normal velocity of my inflow object gets ignored and
b) nothing is visible or changing in the viewport after the first baking step "Bake Data" - no Flip particles are created, but those are probably different tasks)

Using 2.82 Alpha buildbot build 2020-01-07 16:11, hash 55daa0d44483

Spray, Foam and Bubble simulations shouldn't be the same. there's a conference by Sebastián Barschkis on Blender's YouTubes where he shows how it works. Velocity doesn't work for me for liquids inflow either.

There is a Combined Export setting that is supposed to distinguish if particle systems of secondary particles are merged into one cache or not.

By default it is Off and there should be 3 particle systems with 3 different caches.
But it looks like this setting is ignored. And whatever choice is set ; all types of secondary particles are always merged.

@Jonas (JDMations) I just pushed some updates for the secondary particles. Can you try out the latest Blender version and see if it solves the issue?

@Sebastián Barschkis (sebbas) i'll try it thanks for the help