I've got the same problem with my controllers as well. I have 2 controllers connected one by one. Sometimes one of them stops to work but sometimes they stop both. I mean lighting, the fans continue to work normally.
For me there are 3 ways to get them back to work :
1. Replug power connector.
2. Change USB-port.
3. Change controller number by switches on their case.
One method may be enough in some situations but sometimes you have to use all of them.
Also I've found the controllers works more stable if I completely switch off my PC by the switch on my power filter.