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If you're using text logging format, just delete the file. For instance, in a Run Program step:
%DOSCMD% del "%LOGFILE%"
For XML format, that won't work since it won't be a valid XML file if you delete it mid-build. You may want to put the 2nd part of the build in a separate project (which uses a different log file) and call from the first with a VisBuildPro Project action.
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