Why is that a problem? *when* the banishes are performed has nothing to do with determining the boss.
It's important for guessing likelyhoods in ambiguous cases.
For example: two banished of A, two banishes of B, 1 monster left:
1) If it was banish 2*A, 999 fights, banish 2*B, then you could have seen
- with initial 3A, 2B: 66% of B, 33% of A, boss is A
- with initial 3B, 2A: 100% B, boss is B
2) If it was banish 2*A, banish 2*B, 999 fights
- with initial 3A, 2B: 100% A, boss is A
- with initial 3B, 2A: 100% B, boss is B
3) If it was banish 2*B, 999 fights, banish 2*A
- with initial 3A, 2B: 100% A, boss is A
- with initial 3B, 2A: 66% A, 33% B, boss is B
4) If it was 999 fights, banish 2*A and 2*B
- with initial 3A, 2B: 60% A, 40% B, boss is A
- with initial 3B, 2A: 60% B, 40% A, boss is B
60%:40% is not far enough from 66%:33% for observed rates to distinguish them; so you have the following groups, discounting the unambiguous "seen 100% of $AB -> boss is $AB":
group I:
66% B, 33% A, boss is A
60% B, 40% A, boss is B
group II:
66% A, 33% B, boss is B
60% A, 40% B, boss is A
So you still can't tell whether the boss is A or B, unless you saw 100% of one.