So, I just ran into a variation of this problem and was able to connect it to a different issue. Posting it here, in case somebody else comes looking for the answer. My Pebble 2 would randomly lose pairing, and couldn't be reconnected without fully resetting the phone.
Around the same time, I noticed a seemingly unrelated issue with my Twitter app. Each time I refreshed after the app had closed in the background, it would take a bizarrely long time to load in content. White screen, blue circle, at least 15 seconds of waiting. Worst of all, it would close any background processes I had running at the time. At first, I only noticed that it was killing any Spotify stream I had going while browsing the app. But after a few days, it dawned that this could also be responsible for my watch issue.
So I looked up how to solve the Twitter problem, and it was very easy. Just went into Settings > Apps > Twitter > Storage, and clicked Clear Data. This keeps all the account info, but reset my syncing preferences in a way that alleviated the issue.
Hope this helps somebody.