Is there anyway to "move" the FAT32 partition so that it doesn't "grow" over?
That's the difficult part, I don't think I've ever seen a guide for exactly how to do it.
My best guess, you should use dd to create a "emuMMC" backup. You'll have to look at your emummc_sector setting for Atmosphere to determine where to start from, and then make an image from that starting point to the end of your old microSD card.
Then, prepare your new card. It's your choice how you do this. I make two FAT32 partitions, one is going to hold my SD card contents, while the other is going to hold my emuMMC. Most guides throw it at the end, but I like putting my hidden partition at the beginning of the card so that I don't have to worry about all this stuff if I ever decide to upgrade to a bigger card. Your emuMMC partition needs to be at least as big as the image you just made. Copy your SD contents to one partition, for the emuMMC partition you're going to want to use MiniTool or some other tool to find out what sector it starts at. You're going to need to change your emummc_sector setting accordingly. Then, use dd to overwrite the partition with the image you made earlier.
Now, why do most guides put the hidden partition at the end of the drive? Well, since it's listed first in the Master Boot Record (MBR), the Switch (to be more exact, Horizon) will try to mount it and use it, corrupting your emuMMC. So to avoid that, go into Disk Management and simply delete the partition! It sounds a little crazy, but it won't wipe the actual data you copied over, it just deletes it from the MBR. After this, it should work fine, I've been using my Switch this way since Atmosphere first released emuMMC support, and I've had no problems whatsoever.
More info on how that works:
https://gbatemp.net/threads/emummc-setup-win-linux-quadboot.541152/page-4#post-8682981 (we're basically doing the third dash under "4 solutions")
Hope that helps!
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Just to clarify, if you do follow my instructions above and decide to put your emuMMC at the beginning of the card, in the future if you wanted to upgrade again you could simply clone the card, then grow the FAT32 partition to the end of the card, and it won't affect your emuMMC because it's at the beginning!