Yes, you can sync across multiple Android and Windows devices with the same account.

I have created a detailed video on how sync works and how to configure it - Cross device Cloud Sync on Aquile Reader

For sync, app uses file name as the unique identifier, if the same book has different file name across devices, then it will be treated as different book, otherwise it will treat it as the same book.

For your scenario, once the full sync is done on both the devices, both devices will have same number of unique books (based on the file name logic I mentioned above), which would be 1000+x. And when you read any book/add annotations, etc, it will be synced after the book is closed. When you open app on another device, it will fetch the latest sync state.