It’s because the last cd you make is to the root game directory. You need another cd to the directory in which server.cfg resides.

:loop
@echo Clearing Server Cache Files
cd /d (mylocation)
rd /s /q cache
@echo off
cls
@echo Hit Enter In This Window To Restart Server Immediately, Keep This Window Open For Automatic 6 Hour Server Restarts.
cd /d (mylocation)/directoryWhereServer.cfgIs
start “Server” (mylocation)\run.cmd +exec server.cfg
timeout /t 21600
taskkill /f /im FXServer.exe
@echo Server Shutdown Successfully.
taskkill /F /FI “WindowTitle eq Server”
@echo Server Is Restarting Now.
goto loop