client side rules will apply on the BB at their leisure. the mail will probably land in the messages folder and then the next time BES scans the mailbox, it will move it to the folder that outlook moved it to.
BUT, that only applies to subfolders of you inbox. BES cannot manage anything put into a .PST file because it does not reside within your e-mail box. Your BB will leave the message in your messages list if it cannot find where it went in the exchange mailbox - this is the same issue people see when they do hard deletes.
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~Di~
Windows 2003
Exchange 2003
BES 4.1
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