The projects in a solution that will be built by the Make VS.NET action are determined by the Configuration Manager dialog (&Build | C&onfiguration Manager), not the Batch Build dialog (&Build | Ba&tch Build). So you could just check the Build checkbox in the Configuration Manager for all projects/configs/platforms and save the solution.
That information is indicated in the .sln file by the existence of a line like
{GUID}.config|platform.Build.0 = config|platform
for each row with the Build checkbox checked, so it would also be possible to automate munging of the .sln file to add any missing lines (see attached sample).
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