When I make PCBs I like to do multiple projects. Typically you can get a lower cost if you fill out a panel or use all the area you are paying for. On my first KiCAD ver 5 multi project I included 11 different projects. I completed the schematics then the layouts. Two of the boards had copper pours on the back side using the GND net. The individual boards look fine with vias and pads having thermal connections to the pour. Then I copy all the boards and past them into a Multi-Project board. I only copy the layout and do not re-annotate. Generated the gerbers and off to the PCB fab house. When I got my boards back I noticed all my GND pads are not connected to the ground plane. Bummer!!!
Somehow without the schematic and netlist present in the project the GND nets get dropped and I lost my connections. Everything else looks fine.
This is an example of why I think PCBNew isn’t the right tool for panelizing. This is a task that is best done at the gerber level. Unfortunately, I don’t know off the top of my head of a gerber editor that can do panelizing, adding things like routing, mouse bites, v-scores, trimming layers to edgecuts, etc.
Mistakes happen. I had a similar issue with a board that I modified for my first electronics industry employer. We even missed it on the photoplot proofs that we insisted the PCB vendor provided us to make sure our intent made it to the photolith film. I think what saved me from major recrimination is the photoplots went through our full process and were signed off by the engineer.