Ereader

In the folder view in KOReader, swipe down the top menu, pick the tools menu (the crossed wrench and screwdriver), choose "Cloud storage", and then tap the plus (+) in the top left.
You can add a WebDAV server from there, and browse it to download files onto the e-reader. If you want to update a local book just download the new copy overtop it, the reading state is stored beside the epub itself so KOReader should still remember where you were unless the new version of the book is drastically different.

My personal reading tracker is still syncing by pushing epubs using scp directly from my desktop, still haven't had the time to build the plugin for it that I planned, but I've entirely rewritten the tracker instead.
Replicating this can be done by configuring SSH in KOReader, which is done under the settings menu (the cog), "Network", and "SSH server" on the bottom.