Deletion of items in the source mailbox has not been synchronised to the target mailbox.
Deleted items are synchronised using standard sync processes, i.e. via PSTs created by the MSA. If deletions haven't been processed into target there are a number of possibilities.
Check in the config.ini file located on the source server in the \Mail Source Agent\ folder that the default setting "SyncDeletedMessages=1" is present.
Resynchronisation of the mailbox will attempt to sync all data from source, including deletions where there still remains a tombstone of the deleted item in the Exchange system.