Should we migrate files?

Should we migrating away files away from Parse's S3 bucket, or is this not necessary? If so, is there any written documentation on how to approach it?

At some point yes, you should migrate files away from Parse S3. We're working on a tool and documentation on how to do this. Stay tuned.

Any new files saved from running your own parse-server, are saved in your mongo instance or your own S3 bucket if you use the S3Adapter.