How To Get Separate .pro Directory?

I am using KiCad 5.0.1 on my Ubuntu 18.04.1 OS and use P&V 6.0 to keep track of part numbers and drawing/document numbers. I have the following scenario.

I did a schematic diagram of an overall project that consists of a Front Panel, Rear Panel, and a printed circuit board assembly (PBA). Those parts mounted to the Front Panel were assigned ref des prefix A1, those parts mounted to the Rear Panel were assigned ref des prefix A2, and the PBA used ref des prefix A3. This Top ASSY started as Me10019.pro with schematic Me10019.sch. Using Ubuntu I copied this file (schematic) over to Me10022.sch; deleted all parts with ref des prefix A1 and A2; leaving me with the parts with ref des prefix A3, the PBA.

I ran CvPcb assigning all the land patterns/footprints needed and then ran the NET icon producing an Me10022.net file. I opened Pcbnew, did a board outline on the cuts layer, and imported a net file by pushing on the NET icon. Problem is the program imported the Me10019.net file (it didn’t ask which .net file to import) instead of the Me10022.net file. When I first open KiCad the ME10019.pro is at the top with all other files underneath it, including the Me10022.pro file. I didn’t produce the Me10022.pro file, I only produced the Me10022.sch file, so the KiCad program seemed to have produced it. When I check the directory on Ubuntu all files are at the same level, including the Me10019.pro and the Me10022.pro files.

How do I produce an Me10022.pro file that is not under the Me10019.pro file and put all the .sch, .net, etc. Me10022 files to be under the Me10022.pro file?

I make 3 folders for 3 diferent projects.
Then, I copy-paste-rename the needed files from one project to another.

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