I've had this problem on an ad-hoc basis from time to time when installing Airport WiFi networks in Hong Kong. It is frustrating and I really havent been able to put my finger on what the problem is, I do however do the following and it seems to resolve itself..
I quit Airport Utility (v 6.2 620.33)
I then turn WiFi off
I then turn WiFi on
I restart Airport Utility
From what I can figure, and please correct me if I'm wrong is the following.
Airport Utility is constantly polling the devices to make sure they are operational and thus providing any alterts (you can set Airport Utilities up to alert you if there is a problem) to you if something untoward happens.
Airport Utility not seeing a device or having it greyed out on it's console screen doesn't mean there is anything actually wrong with the device. I've had many instances where the WiFi network with multiple AE's and AEx's are on are all operating and downlaoding / streaming but they are either shaded out or have the warning orange light and an exclamation mark against them.
As Airport Utility is constantly polling the device there may be some interference from either an environmental issue or from co-channel interference (most problematic in the 2.4 GHz range). Noise or interference in the 2.4 GHz range could trip the parameters for QoS that the Airport Utility uses. I'm only guessing though.
You may also want to look at what network you are using to view Airport Utility via. It may sound stupid, but if you're using or are connected via a 5 GHz only network or visa versa with a 2.4 GHz network connection and you all of a sudden are out of range of the 5.0 GHz or 2.4 Ghz whilst using the other..... once again polling comes into play.
In short, I give it a kick in the bum and then it seems to play nice, until the next time and then its bum kicking time again.
Cheers,
WiFi Guy HK