This seems like an organizational problem. Maybe:

• Supply each person or group that is responsible for maintaining a 'sub' file or files a custom Perl script for checking the file(s) for which they are responsible. The script begins with
      use strict;
      use warnings FATAL => 'all';
      use vars qw($all $needed $global $variables);
  (some of the fake 'globals' may need to be initialized) and continues with a
      require sub_file_foo.whatever;
  for each sub-file in question. It may be necessary for some sort of fake hash to be built from all the sub-hash-thingies (I don't have a good idea of the organization of all the code in this crazy system) for final verification. Finally, the script prints
      print "sub-file(s) look ok.";
  and exits.
• Establish a 'release date' or 'release number' for each production build. Require each sub-file to have the line
      # checked by Name of dept. XXX on date DDD
  (or "for release NNN", or whatever) somewhere in the file. This means that each sub-file must be modified for each build, but nothing in life is free.
• Supply the person responsible for receiving all these nuttsy-cuckoo sub-files a script that will scan each sub-file received for a given build for the presence of the checked-by line required in the previous step and check that the 'checker' for each department is authorized and the release date/number/whatever is correct for the build.
• Supply the person responsible for receiving all these sub-files a baseball (or, in British-influenced areas, cricket) bat. Place this bat in a prominent position in this person's cubicle or office under a sign that says "For Use On Anyone Who &#@%$ Up A Sub-File For Which They Are Responsible" in big red letters.
• Finally, do all the other checks on the sub-files that you can think of.

That oughta do it.