Your post reminded me that I haven't exported a KML file of my waypoints and routes as of late, going to do it right now so I have a backup on my computer.
I've logged in and out a dozen times as well as reinstalled the app six or more times. If I try to create a waypoint the screen pops up for a second and then goes away. If I then sync that waypoint I tried to make it's on the web but not the phone. I tried the app on a tablet as well as my wifes phone (already installed on both).
When I opened the app on the wifes phone I watched the waypoints disappear and they are gone on the tablet.
This has to be an issue on Garmins end. I saw two post on the Garmin forum from yesterday about this. I was hoping someone else already figured it out and could save me a call to tech support. Yes they are still on the websight.
It's weird alright. If my phones in airplane mode with wifi off the I can create and save a waypoint on the phone. As soon as I turn wifi on the points vanish.
I'll follow up tomm after I speak with Garmin tech.
Got it fixed. What I failed to mention in the OP is I took my mini off my account and added my se to it last week. Even though you can't create waypoints with the SE I still had to sync my waypoints to my SE via the web sight. Then when I synced my phone they all came back.