That sounds very tedious, but in some way every failed solution narrows down the list of possibile causes :P
Do keep us updated, if you want. And you might help the peeps on GitHub by trying out different mobile devices or sync methods, if you really really really want to do something in the meantime. It does seem to be neither your Joplin version nor your encryption setup!
Love the accent colour on the launcher too! Mind revealing what launcher that is? Rofi?Ulauncher?