I tried planting some Bluecap Fungus Seeds in the Dark Lake Shore area about 8 hours or so ago, and I came back tonight after what must have been a reset to find the dirt patches have disappeared and the parent plants are back to the level they were at before.

I think it's working correctly. The dirt patches might not actually get replaced after a reset, but the plants will grow unless they've been harvested/disturbed. Your "other" plants can also keep producing if they're treated well.

I've done some testing, and it's beginning to look like dirt patches are not persistent; only plants. That is, for a plant to actually grow, it must be planted and sprout in the same session. This is naturally not the intention.

Arkov reporting in from afar:

The dirt patches are a cosmetic feature that indicate whether a plant was recently planted there; they appear when a plant is planted and are intended to disappear after a reset. Their disappearance doesn't indicate that the plant that was planted in that spot is no longer growing.

I'll check in later once I've got a free moment to see if there's a deeper issue here.