This post is copy of an "old" answer from Atmel FAQ - currently unavailable. The link still works, it pints to file AtmelAtfwSetup-6.1.133.msi.
This file needs USB driver to be updated. According to Knowledge Base you should download and install AtmelUSB.
Procedure to downgrade JTAGICE3 firmware in Atmel Studio 6.1 SP2 to maintain compatibility with older versions of Atmel/AVR Studio
Question
My JTAGICE3 no longer gets detected in older versions of Atmel/AVR Studio after getting upgraded in Atmel Studio 6.1 SP2. How do I solve this issue?
Answer
The following procedure needs to be done to downgrade the firmware:
Note: This procedure should not be followed if you need to use SAMD20 with the latest version of Atmel Studio.
1. Download and install “Atmel Firmware downgrade” utility from the below link:
http://gallery.atmel.com/Products/Details/c578bdc7-3f6a-4ff1-b2c1-8419ba25dce7
2. After installing, Go to Start menu --> Atmel --> Downgrade connected JTAGICE3 to Firmware V2. This will downgrade the firmware version of JTAGICE3 which is connected to the PC.
3. After downgrading the JTAGICE3 firmware using “Atmel Firmware downgrade”, to prevent Atmel Studio 6.1 SP2 from upgrading your Jtagice3 again, you will have to replace
[program files]\Atmel\Atmel Studio 6.1\tools\JTAGICE3\jtagice3_fw.zip
with
[program files]\Atmel\AtmelAtfw\jtagice3_fwv2.zip
This should make the JTAGICE3 to work with Atmel Studio 6 SP2 as well as the older versions of Atmel/AVR Studio.
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