I also had a problem with Hue devices not deleting in the Alexa app. They were causing a problem because I was getting the Alexa error message "There are a few devices with the name xxx lights, which do you want?" Alexa had zombie Hue plugin devices and new Alexa plugin devices with the same name, so Alexa would occasionally get confused.
Here's what I did to finally make them go away:
1. Disabled the Indigo Alexa plugin by revoking privileges on my Indigo account and disabled the Indigo Alexa plugin
2. Deleted all of my Alexa devices on
https://alexa.amazon.com3. Turned on the old Alexa Hue bridge plugin and created one Hue device with zero lights
4. Performed "Discover Devices" on Alexa--- It found no devices, thankfully
5. Disabled the old Alexa Hue bridge plugin in Indigo
6. Reenabled my Indigo Alexa plugin by authorizing it on my Indigo account and enabled Indigo's Alexa plugin
7. Performed "Discover Devices" on Alexa. It found all my Alexa Indigo plugin published devices and thankfully no Hue devices
8. Went through the Alexa app to set up each device.
I'm not sure if all of these steps are necessary-- but it seems to have worked. This whole experience was rather tedious and frustrating. But the zombie Hue devices are gone and Alexa seems to be linked and working properly. For now.