@mpw I’m sorry you’ve run into this issue, especially after having already uploaded a large repository. We’re working on improving it S3-Compatible Listings - Optimize and Simplify Non-Encrypted Path Support · Issue #111 · storj/roadmap · GitHub
Kopia lists objects using arbitrary prefixes which don’t mix well with storj’s encrypted object keys. To prevent the too many items error you can disable object key encryption Enabling Lexicographic Sorting of Object Listings - Storj Docs. Unfortunately I think you’d need to create a fresh bucket and re-upload your repository using the new credentials.
Did you have any success recovering your existing backups? Perhaps you could copy the repository locally and restore a snapshot from there. Another option would be to setup a self-hosted gateway configured with --s3.fully-compatible-listing Setting Up a Self-Hosted S3 Compatible Gateway - Storj Docs