As far as I know, the sync should not have brought in the exceptions, although I think some other customers have reported the same issue, so we may have a defect here: I'll have to check.
With regard to not deleting machines - can you check how you have got the "When systems are deleted from the synchronisation point" option configured? The default setting is "Leave the systems in their current location", which sounds like what you're describing. You'll need to use the "Delete the systems from the system tree" option.
Many thanks for the quick reply and yes it was that - sorry I missed it.
Never used the epo software before so just getting to grips with it.