Just to keep a default value of the variable. Press Enter to use default from the recent run of your .bat:
@echo off
set /p Var1=<Var1.txt
set /p Var1="Enter new value ("%Var1%") "
echo %Var1%> Var1.txt
rem YourApp %Var1%
In the first run just ignore the message about lack of file with the initial value of the variable (or do create the Var1.txt manually).