Just use $CmdLineRaw or $CmdLine[1] in your second script, so for example:
Script 1
While 1
$nMsg = GUIGetMsg()
Switch $nMsg
Case $GUI_EVENT_CLOSE
Exit
Case $btnYes
Global $Reboot = 1
Run(@ScriptDir & "\PatchDelayRed.exe True")
Exit
Case $btnNo
GUISetState(@SW_HIDE)
msg3()
Exit
EndSwitch
WEnd
Script 2
AutoItSetOption("TrayIconHide", 1)
Global $Reboot = False
If $CmdLine[0] >= 1 Then $Reboot = $CmdLine[1]
If $Reboot = False Then
Do
Sleep(5000) ;Sleep for two hours
Run(@ScriptDir & "\PatchRebootRed_Eng.exe")
Exit
Until $Reboot = True
ElseIf $Reboot = True Then
MsgBox(0, "", "Rebooting Now")
Exit
EndIf