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When a project is created in TE and then a file later removed, the analysis which shows in the project simply has the file removed and whatever analysis was present in the report is deducted from the overall analysis giving a remaining analysis. However, in the case where there was a high level of cross file repetition between the two files originally and then one of those files removed, the cross file reps are still present in the analysis, even if there's now only one file in the project.
