Because each automated analysis is independent of a study, the individual results are stored as separate files. For larger studies, there could be hundreds to thousands of Proteome Discoverer results files. If you save the files to multiple folders, then it might be difficult to find and import these results files into the Proteome Discoverer study for the multiconsensus run.
Thermo Fisher Scientific recommends keeping the result files organized by selecting the same target folder in the Results Path column of the Xcalibur data system. It is easier to create a multiconsensus report from a single folder even if the original injections are distributed across multiple sequences.