The issue seems to come up on a iPhone reset. I have found a couple of things that help to avoid the problem (two weeks so far with no issues). First, if at all possible, I make sure the watch is turned off before the phone boots back up. Second, if I get a message on the phone/watch that Pebble has found a new watch, I immediately reboot the phone again, and while that is happening, I turn off the watch.
Much better than factory reset, which gets rid of several custom alarms. The bluetooth reset has always worked for me as well, but you have to be sure to forget both on the watch, and on the phone (both regular and LE). A pain if you have to reboot your phone a lot (and I have battery issues so it happens when I'm not paying attention), but this eases it a bit.
Note also, if you have not updated to the lastest firmware (which came out just before the merger was announced, consider doing so. It seemed to have helped somewhat. -John