For an OpenEMR instance would consider the database and filesystem (documents directory) to be interlocked (they should always travel together on upgrades and host transfers). If are ever in a situation where need to remove keys then would argue the mistake should be remedied rather than removing keys. At this point those keys on the filesystem will always encrypt passwords in globals (not a huge loss if lose these) and will sometime encrypt the entire log if this option is turned on (would be a huge irretrievable loss if remove the keys).
Check out this post for description on keys (there is a set in database and a set on the filesystem):