This should be accepted as solution. This workaround works, not sure why Splunk hasn't put this workaround in the known issues section in the docs.
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To ensure Splunk fully reindexes a file whenever the datestamp changes, consider using initCrcLength and crcSalt in your inputs.conf. The default CHECK_METHOD = modtime may not detect content changes if the file is overwritten with similar data. Including a unique timestamp in the file or path can also help.
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