The thread is a little old, but do not see where it was resolved. I have had this same problem basically since I started using Cachly a year ago. After I put in a waypoint, (which does show as the current coords, not zeros, when I start.) carefully make sure I save it before leaving the page. I can open it and navigate to the site. Close it and reopen it and everything is okay. But at some point it disappears. I have tested by creating a waypoint, saving it, copying it and pasting into the "Personal Note" section. At some point when I go back the waypoint is gone, but the personal note remains. Maybe when syncing with Geocaching.com it is overwritten? (Because I see the note on Geocaching.com now, but not the waypoint.) Currently on 5.2.13 (2). I just noticed this again. I solved a mystery cache, put the coords in, went and found the cache, logged the find, went home, now the waypoint is gone. If there is other information I can provide please let me know!
ADDED: Not an issue, but often I end up with TWO identical waypoints, and do not delete either of them, but editing one sometimes I end up with THREE, some with original coordinates, then one new one with new/edited coords as if I "Copied" the original and then edited it, but I am not doing that, at least intentionally.
ADDED TWO: Okay, I read what the other poster wrote about closing the app completely, then reopening it. That DID work, I now see the new and edited coordinates. BUT I thought I had deleted the original one since it was just to see if it would stay. So maybe I need to begin closing it completely each time I make a waypoint.....
I do have the official Geocaching app installed also, but not normally open at the same time. I just checked and the old and edited coordinates show up in that app also. Well, I guess I know how to at least see them now if they disappear again. And yes, this is all "live".