Windows scripting scripts (VBS files) run invisibly when they are run by the "wscript.exe" program (which is the default way to run them in Windows). So instead of having your registry entry point to your batch file, have it point to a script. Have the script run the batch file.
Here's a simple one-line VBS script (give it any
name with a VBS file extension) that will run
your batch file invisibly. All you have to do is
replace the name of the YOURFILEBAT with your batch file name:
invisible.vbs
rem ----------------------
CreateObject("Wscript.Shell".Run "YOURFILE.BAT", 0, False
rem ----------------------
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