Since the practical limit to the number of logical files you should combine into a SuperFile is about a hundred, you'll need to periodically run a process that physically combines all the incremental logical files and combines them into a single logical file that replaces them all, like this:

IMPORT $;
IMPORT Std;

OUTPUT($.DeclareData.SuperFile2,,'~$.DeclareData::SUPERFILE::People14',OVERWRITE);

This will write a new file containing all the records from all the sub-files in the SuperFile.

Once you've done that, you'll need to clear all the component SuperFiles and add the new all-the-data-there-is data file into the BaseFile, like this (this code is contained in SuperFile6.ECL):

IMPORT $;
IMPORT Std;
SEQUENTIAL(
  Std.File.StartSuperFileTransaction(),
  Std.File.ClearSuperFile($.DeclareData.BaseFile),
  Std.File.ClearSuperFile($.DeclareData.WeeklyFile),
  Std.File.ClearSuperFile($.DeclareData.DailyFile),
  Std.File.AddSuperFile($.DeclareData.BaseFile,'~$.DeclareData::SUPERFILE::People14'),
  Std.File.FinishSuperFileTransaction());

This action clears out the Base SuperFile, adds the reference to the new all-inclusive logical file, then clears all the incremental SuperFiles.

Re-running the above COUNT action should still result in 620,000.

Once again, edit the code from SuperFile4.ECL to add ProgGuide.SubFile5 and ProgGuide.SubFile6 to the DailyFile, like this:

IMPORT $;
IMPORT Std;

SEQUENTIAL(
  Std.File.StartSuperFileTransaction(),
  Std.File.AddSuperFile($.DeclareData.DailyFile,$.DeclareData.SubFile5),  
  Std.File.AddSuperFile($.DeclareData.DailyFile,$.DeclareData.SubFile6),
  Std.File.FinishSuperFileTransaction());

Once you've done that, re-running the above COUNT action should now result in 1,000,000.