@echo off
mkdir input
mkdir output
for /l %%i in (0, 1, 9) do (
    rename 0%%i input0%%i.txt
    rename 0%%i.a output0%%i.txt
    move input0%%i.txt input
    move output0%%i.txt output
)

for /l %%i in (10, 1, 99) do (
    rename %%i input%%i.txt
    rename %%i.a output%%i.txt
    move input%%i.txt input
    move output%%i.txt output
)