The Dragon ISP programmer I have stopped showing up in Atmel Studio 7. :o This happened just after updating to Arduino 1.6.6, but I also got some new Win 10 updates in the last few days. Anyway this is the ugly workaround I found (linked to from AVRfreeks)
http://atmel.force.com/support/articles/en_US/Workaround/Atmel-tools-not-listed-in-Atmel-Studio-7-in-Windows10
I guess AS7 is going to get an update in a few days or weeks, and I hope I can remember what I did to workaround this.
RANT: this is starting to piss me off if I was trying to do stuff for a boss that was hanging over me it would be looking bad about now.
I feel your pain.
I find it so comical that the programming tools that seem to have the most issues are the official atmel tools.
There is still a very long outstanding bug in avrdude (6+ years) that won't allow you to do back to back avrdude commands on the USB atmel products like avr dragon and jtagICE.
As a result you cannot use the Arduino IDE to burn a bootloader with those devices.
My avr Dragon just sits on the shelf unless I want to do debug wire programming or source level debugging.
For ISP programming my $5 USBasp device is much faster at programming than the dragon and doesn't have the Arduino IDE avrdude headaches.
I do have a version of avrdude that I patched to fix the bug but it is a pain to have to patch each version of the Arduino IDE tools to use it.
So far, over the years, I've been unable to get the avrdude maintainers or the arduino maintainers to accept and pull in the avrdude fix. (It is less than 6 lines of code)
--- bill