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I made a project with two PCB boards. There are two top level sheets, and two corresponding PCB boards for each. The Power supply board is only providing power to board A.
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I have been getting Multiple top level documents has been used error whenever I try to update the PCB boards from the schematics. Is it the wrong way? Is each project file meant for single PCB board?

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In Altium you can only have one top schematic sheet.

From Connectivity and Multi-Sheet Design:

While the project file links the various source documents into a single project, the document-to-document and net connective relationships are defined by information in the documents themselves. A multi-sheet design project is arranged as a hierarchical structure of logical blocks, where each block can be either a schematic sheet or a HDL file (VHDL or Verilog). At the head of this structure is a single master schematic sheet, more commonly referred to as the project's top sheet.

You'll have to make another project containing the Power Supply schematic and PCB documents.

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  • \$\begingroup\$ what is the purpose of having option to add more PCB files in single project? \$\endgroup\$
    – zud
    Commented Jan 19, 2015 at 13:38
  • \$\begingroup\$ Actually, you can have sheets in a flat design: If your design is not hierarchical - i.e. the sub schematic sheets are all on the same level, with no sheet symbols referencing further sheets below - the design is a flat one. So you either have a hierarchical structure with a top sheet or a flat design with only one level of sheets. \$\endgroup\$
    – m.Alin
    Commented Jan 19, 2015 at 13:47

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