@echo off
for %%a in (*.csv) do set /P "header=" < "%%a" & goto continue
:continue
(
echo %header%
for %%a in (*.csv) do findstr /V /C:"%header%" < "%%a"
) > large.txt
ren large.txt large.csv
EDIT: Below there is an example of what this program do:
C:\Users\Antonio\Documents
>type file1.csv
Common header for all files
File One line one
File One line two
File One line three
C:\Users\Antonio\Documents
>type file2.csv
Common header for all files
File Two line one
File Two line two
File Two line three
C:\Users\Antonio\Documents
>type file3.csv
Common header for all files
File Three line one
File Three line two
File Three line three
C:\Users\Antonio\Documents
>test
C:\Users\Antonio\Documents
>type large.csv
Common header for all files
File One line one
File One line two
File One line three
File Two line one
File Two line two
File Two line three
File Three line one
File Three line two
File Three line three
type *.csv >newfile.csv & newfile.csv?