This is a headache and I don't like it. I'm done.
I absolutely understand. You are clearly frustrated... and the results are showing you are trying to get it over and done with by the short cuts.
Whether you need a break or want to push on... there is NO expectation for you to continue stressing yourself.
(I unfortunately cannot help cause you didn't have both versions. I have all the saves still with the least amount of variables being changed by catching all these Legendary doodoos.)
The testing we did was over two days JUST narrowing down the Rematch Bools for the first 3 Regis. We noticed going from catching a single 1st Regi (Tests 1-3) to catching a save's 2nd Regi (Test 4-5) that the amount of story flags increased from 2 to 7... there's even more with the 3rd caught.
TEST 1
59457960 - Bool2 => Bool1
B213C388 - Bool1 => Bool2
EE1FD86E - Bool1 => Bool2
TEST 2
59457960 - Bool2 => Bool1
B213C388 - Bool1 => Bool2
DAB3DD3A - Bool1 => Bool2
TEST 3
59457960 - Bool2 => Bool1
B213C388 - Bool1 => Bool2
EE3F84E6 - Bool1 => Bool2
TEST 4
086EE81F - Bool2 => Bool1
194DB28D - Bool2 => Bool1
1E7EAB83 - Bool2 => Bool1
4269F80E - Bool2 => Bool1
6198B4E0 - Bool2 => Bool1
8909C446 - Bool2 => Bool1
B213C388 - Bool1 => Bool2
D249A548 - Bool2 => Bool1
EE1FD86E - Bool1 => Bool2
EE3F84E6 - Bool1 => Bool2
TEST 5
086EE81F - Bool2 => Bool1
194DB28D - Bool2 => Bool1
4269F80E - Bool2 => Bool1
6198B4E0 - Bool2 => Bool1
8909C446 - Bool2 => Bool1
B213C388 - Bool1 => Bool2
D249A548 - Bool2 => Bool1
DAB3DD3A - Bool1 => Bool2
EE3F84E6 - Bool1 => Bool2
There are just so many story beats testing one Stationary Legendary Pokémon one after the other on a single save to easily hit the right result. The right story Bool being edited at the RIGHT point on a save will have the desired effect but be useless to most others and yourself once you progress too far in that story.