The workaround would be to skin a IXB as an IXA, then disable the mod when you actually upgrade to an IXB later in the game.
If you're trying to get a IXB available from 1939 the best place to start would be my XXI 1939 mod - it does exactly what you're trying to do but with an XXI so if you adjust the files that I adjusted you'll be on the right track.
There's also a number of notes written into the files. If you don't want SH3 to read what you put into a file you preface the line with ';', so wherever you see a ; it is either the old value that has been retained (in case I screwed anything up) or a note, for example the type of torpedo that I have changed. Some of bbw's original notes are also in there but you need to be a GWX 3.0 user or you'll need to use your own base .cfg files.
Feel free to use my mod as a base for your own.
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