Dev, thanks for the suggestion. Last night I managed to find a work around.
It must be actioned from the users windows profile and outlook profile (as opposed to adding the users mailbox you the admins outlook profile).
Exporting the migrated Calendar entries to a .pst file and then importing them again (you have to make sure duplicates are overwritten with the ones that are imported) seems to place them in Outlook/exchange in way that the BES can see them as new entries. It then sends them down to the handheld.
It is a workaround not a fix, I am still awaiting a fix from Quest for this issue. The only other comment I have is that it will not send down entries prior to the current day.
Dev, thanks for the response.