Poor co-registration limits Sentinel-2 time series analyses (at pixel level)

In this case I think the best solution is to apply Principal Component Analysis (PCA) according to the results, you could re-sample the granule to the highest resolution band of the component, But putting in mind that the re-sample for instance from 20 to 10 m doesn’t retrieve the objects they already aren’t existed within the 20. For more details,

Please have a look at the following post, Re-sample Meaning

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