This is going to sound soooooo '80's but... your EXE file sounds pretty crude, too, so I'll give this a whirl:
There is a DOS way to do this. Have you ever written a "Batch file". They still work through the command line in Windows.
The essentials of the *.BAT file will be to give a sequence of DOS commands in order to accomplish the task. The routine will first copy the EXE file to each folder in turn, run the EXE, direct the output of the EXE to a text file, rename the output file to contain a trace of the folder path, move the text file to a folder where the rest of them will be stored, then move to the next folder and repeat.
CD C:MD A\listfolder
...
copy C:\A\thing.exe C:\B\folder
cd C:\B\folder
thing.exe > list.txt
ren list.txt list_B_folder.txt
move list.txt C:\A\listfolder
del thing.exe
CD c:...
You don't have to type this a thousand times. You just have to type it once, and use something like a spreadsheet to duplicate the command sequences, updating the applicable folder path each time. Then extract from the spreadsheet a text-only version of the commands (clipboard & notepad).
When finished, you will have a hundred text files that you can concatenate.
Yes it sounds crazy. You only have to do it once, right?
STF