Talk about 'Don’t try and fix something that’s not broken'

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Decided to rip out the chip on the Ex Met Plod project (FL 3.0 2000w) and slap it into one of my other 3.0 FL MV6's for testing, only because the ex plod seems to go like a rocket to me, so was trying to work out if its the Police Chip, lower ratio diff or a mixture of both.
Anyway out comes the ECU, done this loads of times before be the way, the ECU ends up on the desk, next minute, phone calls and emails re work, cut a long story short, I gets side tracked with other things and the ECU ends up staying on the desk for a couple of days.
Plugged the ECU back where it belongs this morning (un touched), started the plod, fine, went for short spin, seemed a bit sluggish and starts stalling at tick over?, restart takes a couple of attempts and the revs at tick over are all over the place?.
I've re sited the ECU a couple of time since, and checked inside the black box for any disturbances, still the same on tick over, the Car was running sweet before I pulled the ECU.
I realise that the ECU will probably have to re learn, but this isn’t right!
Any thoughts please.
Chris.
edit, Forgot to mention, No faults thrown on the Paperclip.