Let me tell you my story: I had the same issue, very frustrating; even more, after upgrade the unit it came freezed, not worked at all. I tried different ways and nothing worked. At the end this is what worked for me and I'll share it, maybe it works for anyone else:
1. I donwnloaded the FLASH MEMORY from the Line 6 site:
https://line6.com/software/index.html
I donwnloaded every (just in case) Flash Memory files:
2.62.00 (the last one), 2.32.00, 2.31.00, 2.21.00, 2.20.00, 2.10.00, etc...
2. I turn on the POD pressing down arrow.
3. I launched the last version of Line 6 Monkey
4. I make sure to have the last version of drivers
5. I select the POD in question (of course) and then, I click on INSTALL FROM FILE.
6. I choose 2.32.00 FILE
It seems that it is a issue with the 2.62.00 version.
That worked for me. I needed to do this a couple of times. I hope this helps you.