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Kavita
Kavita is a fast, feature rich, cross platform reading server. Built with the goal of being a full solution for all your reading needs. Setup your own server and share your reading collection with your friends and family.
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InfluxDB
Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.
Is OPDS an option on both devices? If so, perhaps something like dir2opds would suit your needs?
I'm currently using Kavita to manage my epub library. It works sort of like Jellyfin for ebooks, where you can point it to a folder or share on your network and have it index the files. You can download, read and sync progress across devices, but unfortunately no notes feature yet. I think it's still pretty early in development though.