You're on the right path. Just select the controllers you want to export for each SD card. Each one will start at one. That's fine. Just set up each controller to match.
One thing I'm a bit unclear of in your description though is whether you plan on streaming the data to the ESP32s from the FPP, or just using multisync and having it play local data. The latter makes more sense.
Channel numbering is always relative. Multisync simply transmits sync data. It basically says, "Playing XYZ sequence, current frame 12345" The slaves then make sure they're playing the sequence with the matching name, and at the same point in time. What is contained in the sequence files and what channels they go to is irrelevant to the multisync process. Because the ESP32 is a relatively resource limited microcontroller, you don't want to give it lots of extraneous data to sort thru. You only want to have the channels that are relevant to the pixels you're controlling. It doesn't matter how that channel range fits in to the whole overall sequence, it only matters with respect to the sequence file and the string it's going to. So each ESP will be set that its output starts at 1. It will be different data, because you put different data starting at slot 1 to each fseq file.
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