Hello. This is what support told me when I contacted them with this EXACT issue:
"Hi, This is unfortunately how the looper currently works. But, a workaround is to use the 1 button looper which can exist on the stomp box panel. Using the 1 Switch Looper: Add a Looper > 1 Switch Looper block to your preset and assign it to a stomp footswitch.(Adding a 1 Switch Looper to HX Effects from Stomp view automatically assigns it to the selected footswitch.) Press the 1 Switch Looper switch. The LED lights red, indicating the loop is recording. Press the 1 Switch Looper switch again. The LED lights green, indicating the loop is playing back. Press the 1 Switch Looper switch again. The LED lights amber, indicating the loop is in overdub mode. Subsequent presses of the switch toggle between play and overdub mode. While the 1 Switch Looper is in play or overdub mode, press and hold the switch for 1 second.The most recent recording is undone. Holding the switch again will redo the recording. On Helix, Helix Rack/Control, and HX Effects, “UNDO” or “REDO” briefly appears on the scribble strip. On Helix LT, “UNDO” or “REDO” briefly appears in Performance view. Quickly double-press the 1 Switch Looper switch.Playback/recording stops and the LED lights white, indicating a loop is in memory. While Looper playback/recording is stopped, press and hold the switch. The recording is deleted and the LED lights dim white. Let me know if you have any more questions. Thanks, Will - Yamaha Guitar Group Support"