New Update fixes this issue !!
HELIX FIRMWARE v1.04.3 RELEASE NOTES
IMPORTANT! Before restoring your backed up presets to Helix, you must first install the latest version of the Helix application!
Helix v1.04.3 is a free firmware update that includes fixes, stability improvements, and optimizations. It is highly recommended that all Helix users perform this update!
It is also recommended that you back up your current presets by using the Helix application to create a preset bundle, allowing you to install new presets as part of the update process.
The easiest way to perform the update process is by installing the latest version of Line 6 Updater. Once you've connected Helix to your computer via its USB port (hubs are not supported), Line 6 Updater will recognize the unit and take you through the update process. The Line 6 Updater application may be downloaded here: http://line6.com/software/
In rare cases, engaging the expression pedal toe switch may cause the 1/4" and XLR outputs to stop passing audio, while the rest of the unit appears to be functioning normally. Audio could only be restored by turning Helix off and back on again â€”FIXED
General stability improvements
Other minor bug fixes and optimizations
RESETTING HELIX GLOBALS
IMPORTANT! This procedure will completely overwrite all existing presets and setlists, as well as clear all user IRs and reset all global settings! Back up your presets and IRs before proceeding!
Turn off Helix.
While holding footswitches 9 and 10 (middle two switches on the bottom row), turn on Helix. Wait for the message â€œWill reset Globals and restore stock Presets, Setlists and IRsâ€¦â€ to appear and let go.
Assigning a custom label to the EXP Toe Switch scribble strip disconnects wah blocks Position parameter from EXP 1; can be manually reassigned
Pressing BYPASS while viewing the Model List > Looper category can invert Looper footswitch behavior
Saving a preset to a new destination may display the wrong preset name until it's reloaded
While a loop is playing, changing from a preset with the Looper block on Path 1 to one with the Looper block on Path 2 may cause a small portion of the recorded loop to play
Minor pops and clicks may be present when Helix is streaming audio from a MacÂ® running OS X 10.11.1 (El Capitan)
Minor pops and clicks may be present when Helix is streaming audio from an iOSÂ® device running iOS 9 with AppleÂ® Camera Kit
Importing a Helix bundle while streaming audio over USB may cause the Helix application to disconnect
In rare cases, Amp+Cab or Cab > Dual parameter graphics may overlap the action panel buttons while in Pedal Edit mode
Changing a delay with note subdivision time will unsync resultant delay time from Preset/Global BPM