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Adding to the discussion:
The protocol used for Sync should be
As protocol, WebDAV comes to mind. It sure has issues but is well known and established in the open source community. Downsides are the high complexity of the protocol (afaik). Perhaps there are better alternatives.
For Sync, not only a file transmission / storage access protocol is needed, but also a sync protocol, that compares files. Here we can perhaps learn a lot from Syncthing.
In case Sync screws up, there should be an option for automatic backups.
Hi! May be you don't have to develop sync by yourself and just look at Seafile integration for selfhosted solution. Seafile does already support markdown edititing and preview, has git-like engine with version control support and it very mature and stable. May be you just can provide an integration mechanism with it. That way you can also free your resource to make Notable more mature and powerful and concentrate forces on mobile apps. And may be to add more features to desktop apps like alarm or notification by time. Please consider to look at Seafile.
P.S: You are doing nice job and the excellent product!