You can use the append board button. It is in the top left side of the screen. It goes hand in hand with schematic sheets. But a good workflow helps in preventing errors.
I recommend reading this post of mine. It explains in great detail how I append boards.
You may want to re-annotate your 3 projects beforehand to avoid annotation overlaps. But it could also be solved after the merge.
About that error. I have it too alot, but this error occurs when I copy paste a mounting hole of which I deleted the silk REF text. IMO it is a huge payne, and I for one could live without this particular error. But I suppose it exists for an important reason.
This week I was working on a panel containing different versions of the same layout.
I did not have the time to learn how to use KiKit for multi-pcb panelization, so I was basically copy-pasting the boards in the panel, did not realize there was a board append button. It is a much elegant solution, since net names are preserved.
The only disadvantage is net names are duplicated across boards. Is there a way to automatically add prefixes or suffixes to the appended board nets, so nets are independent? That would be the perfect solution.
not that I know off. I would make the unique boards first, like you propably have already. Than run DRC and fix errors.
With same net names, it matters little whether you use copy paste or append board. I do recommend grouping each board to avoid losing a track or a via. Make the panel and don’t bother with the DRC.