scousefly

Just found out that my big end bearings let go (WRX 48000), obviously a new short block an engine build required which in turn means evrything outta the engine bay and battery disconnection.
When I get it back I have to run the engine in for about a 1000 miles/3500rpm
what happens to the ecu?
I take it will be back to the start when the rebuild takes place but as I can only go upto certain revs during run in do I need to disconnect when the after run in oil change is done so I can get the best outta the superunleaded?
What is the correct ECU reset procedure?