(A) - Soon as you place a bet (matched or not) it is given a Bet Reference - yes ?
Correct.
(B) - Then if you were to change (increase) the stake the bet is split into two and it appears as two placed bets (the original stake and the new stake) with two different Bet Ref Nos - correct ?
Correct.
(C) - If you had two Excel spreadsheets running in one BA session and Bets were submitted for the same selection at the same time would the system recognise this as one big bet (and lump the stakes together assuming they were both similar type of bets i.e. both Back or both Lay bets) or would it see it as two separate bets and give them two separate bet references (which is what I think will happen) ?
They will always been seen as separate bets.