I spent weeks building the turn and was nearly finished when these updates came out, so I was like "Oh, Noes!!"
Something that might save you from frustration in the future.
Pick the scenario you want to use. Load it into the editor and then “Save Scenario As…” some other number greater than 25. If you are dinking with Scen02, then save it as Scen42, put a name in the Comment field like, “Hakko Treetop”, or something. Be sure to also copy the aei002-(01 to 16).dat files to aie042-(1 to 16).dat. The editor won’t do it for you, it will copy (rename) only the top level aei002.dat file.
Now you have Scen42 that is identical to Scen02, but does not have the restrictions that are imposed on Scens01 – 25. Now you can update it just like you can do with a mod.
I keep the regular stock cenarios in a renamed 'Scen - Matrix' folder for reference and back-up, but the game's SCEN folder contains
Scen41_War in the Pacific_The Full Campaign
Scen42_War in the Pacific_Hakko Ichiu
Scen43_The Battle of the Coral Sea
Scen45_The Thousand-Mile War
Scen46_December 8_The Full Campaign
and so on.
This makes it very easy to update things for any errors that crop up, as well as capture systematic changes like the AAA and ASW things. Very easy to also add things like AndyMac's updates. A good way to proceed if you play the AI. If you play H2H or PBEM, all that's required is trust between the players that nobody is gonna sneak something in (or out).