Since version 2016 R3 Rebex SFTP supports the 'check-file' extension of SFTP protocol.
To get the remote file checksum, just use the GetChecksum
method.
string remoteChecksumMd5 = sftp.GetChecksum(remotePath, ChecksumAlgorithm.MD5);
string remoteChecksumSha256 = sftp.GetChecksum(remotePath, ChecksumAlgorithm.SHA256);
See more code examples at
http://www.rebex.net/sftp.net/features/single-file-operations.aspx#checksums