I don't have a Helix, I have a Solix and Apex units. In the past I have experienced a similar problem when upgrading. What I did that worked for me was I downloaded the software into a separate file on my desktop computer. I then unzipped the file. I then reformatted my 32k card before copying all of the unzipped files from the desktop file. I think the key for me was the reformatted card. Upgrading can always be an adventure and a challenge. Good luck.
Formatting the SD card was the solution.
All updates worked without problems.
(Btw, fast format is sufficient.)
Thanks to 9Phil for the solution.
And also thanks to Rickie for the fast responce.
Regards
Wolfgang
P.S.: maybe it would be wise to add this information to the Humminbird update instructions.