Track provenance - The documentation of your study is best done during the process, not after.
Changes made to the data to correct errors should be described during the data manipulation process by the person making the changes.
Seeing the changes made in a data file or record is easily done by software but knowing why those changes were made is a job for scientists.
Documentation applied to the differences in data is known as provenance metadata.
You can apply this information at the file level or at the record level but what you ultimately seek is an unbroken chain of provenance from the source to the most recent version and right on out to the active or archived version.
Provenance metadata can be recorded in a very structured fashion or in a narrative form. There are no standards and no good guidelines for recording provenance in the environmental sciences. There are disciplinary approaches that have been used for decades but best practices have yet to emerge.
So record what you do, when you do it, and why you did it, when processing your data. Documentation is required to ensure the longevity of data. Most ecological metadata is based on recommendations contained in Michener et al. 1997.