I have been doing the same routine for 3 months now with a stable situation all the way through FW 10. I have been using GC mobile on my WIn 10 mobile phone (Nokia Lumia Icon) with great results including an update yesterday post run. I came home and connected to my pc to check sync and any updates. Later attempted to connect to my Fenix 5X with the phone to no avail. I have done everything to remedy to no avial last night and this morning. From uninstalling GC and removing traces of Fenix from phone. Doing a reset to default on the watch. Speaking with support this morning and reinstalling a prior release on the fenix from a file he emailed me. Still no results connecting to phone. I am able to connect wired as well as sync wirelessly to my network. I simply cannot connect to my phone though it does see the Fenix and will pair with it. GC mobile also sees the Fenix but will not connect.
It sounds like your watch is working overall. I would look more at your phone. Windows Phones are not exactly mainstream and it sounds like that is were your issues are. Have there been any updates to your phone or the other apps installed on the phone? Do you have another phone to try?
Early yesterday afternoon I was having issues with the phone and Garmin Connect. This was one hour after syncing a run at the trailhead on my phone successfully. I thought maybe the phone was self updating when at home and there was a phone update downloading. I assumed that was the culprit. Windows 10 mobile sent an update to all mobile devices yesterday so my phone had a clean install of that system update. The issue began an hour before that though. When I came home I plugged in the Fenix on my pc to update some settings since I really exceeded my max HR. Was after this I was trying to look over and check GC Mobile was showing the right settings when I found I could not longer pair with the app.
Unfortunately I have no other phone to test. I do have a Garmin Drivesmart 51 though and just made a phone call through it with bluetooth enabled and paired with the Nokia. I can also pair with my DeLormeSE, the old one though I think the Fenix uses ANT+ with it's Min/Fenix Widget. And no Earthmate App for windows phones.
*Solved this doing a complete reset of the phone. GC then asked to pair the 5X.