For the external SD card, Kobo expects there to be a single partition (partition number 1) and FAT32 filesystem. The internal SD card has three partitions (1 root, 2 recovery, 3 user data), when you hook it up to USB you only get a view of partition 3.
It's possible to create a 4GB partition/filesystem on a 8GB card. In particular this happens if you do a 1:1 copy from 4GB to 8GB card without resizing the copy.
Resizing partitions is not something the Kobo is normally able to do by itself, I had a mod (Magic Memory Upgrade Mod) that does this for using Kobo standalone to upgrade the internal card without PC assistance, but I haven't tested in a while if it still works.
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