When I am sitting at my computer, I get/read/delete emails as per normal, but even if my Berry is turned off its still gets a copy of my emails that I have deleted (BIS/IMAP). Is there a setting someplace where I can set to say, if email has been deleted from server do not copy to Berry?
Unfortunately you can't get full reconciliation on BIS in most cases. The state of your BB is irrelevant. BIS will collect mail whether your BB is on or off.