I'm not sure if this answers your question but in an EasyEDA Project you can have a schematic spread across any number of schematic sheets from which you can generate a single PCB for all the sheets.

You can do Convert to PCB any number of times and generate a different named PCB each time by saving them with a different name. Subsequent to this, you can do Update PCB for any PCB because you will be asked which PCB to update.

You cannot however have different schematic sheets in a Project and convert each sheet into a separate PCB because on doing Convert to PCB all the sheets in a project are assumed to go onto the same PCB.

Given those constraints, here's what I think you will need to do:

1. Split the design into separate schematics, one for each PCB.
2. Put each schematic into a separate Project.
3. Convert each of those schematics into PCB.
4. Then you will have a complete Schematic, BoM and PCB each in it's own Project folder.

@andyfierman Thank you, I kinda hoped that it would be posible while having it all in one project (because it is one project) or filter them out after the importing.