About the ending:
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MC wants so solve their problem by creating an endless loop, Amelie by a quick death.
MC used the bark from the tree to create medicine that induces memory loss, which they can do as a pharmacist. As Amelie suspected it to be poison, MC had to take it too. To not appear suspicious from the memory loss, and to still continue the plan every loop, they wrote down a conversation (which they did in the first loop, long before the start from the view of the reader. If you read the first lines again, you see they don't know Amelie, because they already have memory loss).
To keep the endless loop going, they have to make more medicine every few loops. And after an even longer time, to regrow the tree, which grew old and had little bark left, so they buried seeds.
What it means:
It's a metaphor for how people deal with having a life they consider void of meaning and purpose ("driving a boat through emptiness"). Many people fall into self-destructive, purely pleasure seeking patterns (like doing reckless extreme sports, or taking illegal substances), others into obsessive repetition (work all day, then eat the same food, watch the same show, never do anything new because it is dangerous).
And while those sound like two opposites, and the second group feels morally superior to the first, is it any different? They might technically live longer, but to me it's just as self-destructive. Both are just distracting yourself.
So the "solutions" of both characters are supposed to be dissatisfying to the reader. I want the readers to think "pull yourself together, and work to find your way back" (so to find meaning in your life yourself). Because even if it is hard, it is something we all have to do at some point.