That far in the future and they forget the "Cut" and "Paste" commands

[cantremember]

My interpretation is that brainscans are indeed almost like a computer file, once the scan is stored. But a scan, while a digital representation, contains so much information that the computer can "run" the information in a simulation model so accurate it behaves the same was as the physical host, to the point it actually possesses the same ammount of conciousness.

I think when Simon sits in the seat at Omicron, supposedly another copy is taken, and the seat not being hooked up is an oversight by the map maker.

Also while you can delete brain scan data, Simon doesn't seem to feel too bad about it, since they are flat files and in a "frozen" state, there is no conciousness when they aren't being "run".
But killing Simon requires physical destruction or intervention, I don't think Simon-II could just be frozen and deleted during the copy-process in the pilot seat.