I recently had to tackle this problem, and many files that I wanted to move to from the hierarchy to a single folder had the same name as each other, and I wanted to still flatten the hierarchy without them to being over-written.
What I did was write a script that moves the file, but renames it with the old hierarchy path in the name
for example:
source files:
C:\files\somefiles\file.txt
C:\files\otherfiles\file.txt
destination is C:\newdir\
files are created as
C:\newdir\somefiles-file.txt
C:\newdir\otherfiles-file.txt
here is the code, batch file 1 goes thru the files, batch file 2 renames and moves them (could also copy instead, if you want to preserve the source:
@echo off
for /r %%f in (*.*pr) do @renameandmovefilespart2.bat "%%f" "%%~ff" "%%~xf"
renameandmovefilespart2.bat
@echo off
Setlocal EnableDelayedExpansion
rem set the whole file path
set origWhole=%1
set origPathOnly=%2
set extension=%3
rem here you can set where the directory to hold the flattened hierarchy is
set destDir=c:\destinationDir\
rem set the directory to do a string replace
rem make this the starting directory, that you dont want in the newly renamed files
set startingDir=C:\starting\directory\
set nothing=
set slash=\
rem here you can set what the character to represent the directory indicator \ in the new files
set reaplcementDirectoryCharacter=--
set quote="
rem cut out the starting part of the directory
call set newname=%%origWhole:!startingDir!=!nothing!%%
rem replace slashes with new character
call set newname=%%newname:!slash!=!reaplcementDirectoryCharacter!%%
rem remove quotes
call set newname=%%newname:!quote!=!nothing!%%
rem @echo shortened: %newname%
rem @echo source path: %origPathOnly% newPath: %startingDir%
rem @echo extension: %extension%
rem rename the files
ren %origWhole% %newname%
rem prepare to move the file, clean up the source path
call set origPathOnly=%%origPathOnly:!quote!=!nothing!%%
move "%origPathOnly%%newname%" "%destDir%"