Fix chunked prefill

[hnyls2002]

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Motivation

When the radix cache is disabled, the chunk cache would not update the prefix indices and last node, due to the API changes in #977

Checklist

1. Ensure pre-commit pre-commit run --all-files or other linting tools are used to fix potential lint issues.
2. Confirm that modifications are covered by complete unit tests. If not, please add more unit tests for correctness.
3. Modify documentation as needed, such as docstrings or example tutorials.