Edited to add: In Orgzly Revived go to Settings -> Sync -> Repositories and add https://myfiles.fastmail.com/subfoldername/ (I use "Org")
This version also ships and Android Quick Settings tile that will start Syncthing for those X minutes and stop it outside of that schedule, so I'll hit the button as I'm putting on shoes to go out after making a shopping list on my phone or what have you
You can use more restrictive run conditions, and limit how much time it spends per hour active.
You can also limit it to run only when charging or on specific networks.
[0] https://f-droid.org/en/packages/com.github.catfriend1.syncth...
It very much depends on your workflow. Some people may need to use different org files for quickly capturing notes on both phone and desktop while avoiding conflicts. (Luckily, both Orgzly and org-mode has good support for combining content from multiple files.)
But in general, the git repository type (still in beta) allows two way syncing without unnecessary conflicts.
Synchthing is mentioned often with Orgzly, so I looked into Syncthing. I've been disappointed to find Syncthing drains the phone battery excessively if you enable continuous (event-driven) two-way sync between phone and server.
The problem is Syncthing doesn't hook into the phone's notification delivery service, so it can only pick up changes by keeping a socket open to the server and sending packets often, throughout the day, to keep the socket alive. Even if there are no file changes to report. That drains the battery much faster than, say, a chat app that uses the notification service to send triggers from the server to the phone when there's a new message. (I wrote about technical reasons why that's more battery-efficient here: https://news.ycombinator.com/item?id=38661294).
Does anyone have a recommendation that will keep notes in Orgzly two-way synchronised with Org files on my server, reliably, without draining the phone battery excessively, and without a long delay for changes on the server to propagate to the phone?