You can use /purge option as it enables the deletion of the files and directories fromt he destination tree which do not exist in the source one.

And I would suggest you to provide us the version of EMCopy you are using so that we can investigate the issue that you have reported

Thanks

I should've given these details in the beginning itself.

I am currently using Emcopy-04.14 (last week-incremental update), but I've used the Emcopy-04.10 for initial copies before this(for same cifs server migration).

Sameer, I am using purge option, below is the snippet of all options used:

---------------------------------------------------------------------------------------------------------------------------------------------------------------

EMCOPY 04.14

Copyright (C) 1999-2012, All Rights Reserved,
by EMC Corporation, Hopkinton MA.

System information
==================

Client OS                   : Microsoft Windows Server 2003, Standard Edition Service Pack 2 (build 3790)

Server SRC                  : Source-CIFS-server       5.0 EMC-SNAS:T5.6.43.800
Server DEST                 : Destination-CIFS-server      5.0 EMC-SNAS:T6.0.43.104

Command information
===================

Date                        : 21/04/2012 09:01:19
Source path                 : \\Source-CIFS-server\c$\cifs-fs04\
Desti. path                 : \\Destination-CIFS-server\c$\cifs-fs04\
Files and Dirs filter(s)    : *
Directory options           : /s /purge /stream
List/Modify/Create options  : /d
Security options:           : /o /a /secfix /sd
Thread count                : 128
Retry options               : /r:10 /w:0 /c
Log file                    : /log+:Apr21_emcopy_log.txt

---------------------------------------------------------------------------------------------------------------------------------------------------------------

On destination, many files of 0bytes size have old last-modified dates. So using /d option might ignore these files, but again I don't want to perform the full copy of the filesystem once again. 

One of my colleague suggested to use emc46968, but it is already applied on the destination NAS.