If you run the .bat and it can not find your folder you need to right click the .bat and choose edit with notepad. The line will be in there and you set your directory path there. It currently is set to
powershell.exe -NoProfile -ExecutionPolicy Bypass -File "%~dp0FS25-PreFlight.ps1" add -ModsDir "D:\FS25\mods" or what ever your mods folder location is.