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If anyone has already tried enabling EFS on FileStream data for multiple databases around 500 GB+, please share your thoughts on feasibility or issues / considerations we should keep in mind.

We are in process of enabling EFS for PROD. We are testing in lower environments too.

Specifically, which one is better - enabling parallel EFS, or enabling EFS on one FileStream Folder at a time?

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I can't speak to whether or not EFS should be applied per folder. However, there is a security consideration that seems to be worth an answer here.

Check out this post from David Browne on the MSDN forums question Can FILESTREAM directory containers be encrypted with EFS?:

Note that during a SQL Server backup of FILESTREAM data, the data is stored decrypted. A restore operation to a normal volume therefore will result in decrypted values.

So if you are using native SQL Server backups, you will need to keep this caveat in mind from a security / compliance standpoint.

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