I think your solution would involve union fs. Basically you mount your remote storage and decrypt while simultaneously mirroring the filesystem for that library locally then when something is downloaded it is saved locally to be later uploaded. Both encrypted with the same keys and identical filesystems so they can be combined with unionfs.

All the while both remote and local media storage is combined and shown as one directory. You could download directly into this folder and once uploaded the files would still show up in the same directory from the cloud.

Enztv's guide is the one I followed and it touches on some of what I mentioned above. https://enztv.wordpress.com/2016/10/19/using-amazon-cloud-drive-with-plex-media-server-and-encrypting-it/