It seems there are a string of posts dating back years on this topic and yet people are still having problems.
I had my own issues 3 months back and managed a manual fix to ensure that MFP calorie data was synchronising with Garmin Connect so I could see calories in/out on both apps. However, I now have a message on Garmin Connect (Web version) saying that "Unable to Sync: Right now we aren't able to sync with your MyFitnessPal account. It looks like something temporary, so please try again later".
Well it certainly doesn't seem temporary as it's been like this for days. I appear to be disconnected on MFP (via the Apps section) and when I click on the button to reconnect I end up back on the Calories section in Garmin Connect with the same blue error message. There doesn't seem to be an option to "disconnect" within Garmin Connect (not from what I can see anyway).
Anyone else having a similar issue? Frankly, I am sick to death of both Garmin and MFP for their crappy applications. Why bother creating hardware when the support for analysis online is flaky at best. Rant over...