hi, to fix this, open a single board step file in solidworks. With the assembly open, use file->pack and go, then set the save to folder to someplace else, check add prefix, and set the prefix to board1. Click save.
This should turn parts called C1,C2,C3 into board1C1, board1C2, board1C3.
You then need to open the exported assembly and use it in your top level design.
You have to repeat this for each board.