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I would probably use eppy to do what you are suggesting but if you are familiar with using the command line and using the search and replace across files in a text editor there is another option that could be used.

Create a file that has all the new schedules in it using new unique names for the schedule names. Use the command line to append this new file to the 1000 existing files. Then using the text editor search and replace across files, replace the references to the old schedule names to the new ones (you will have to do this four times, once for each schedule name).

I would recommend that you keep the original set of files and do a file compare using WinMerge or some other text file comparison utility to make sure everything worked ok.