Save your data:

Scrupulously preserve the original data used to generate the graphs included in your thesis, and in every paper, report, or poster. This includes the raw data, the excel data, the graphs, the distilled graphs, etc.

When writing a document, create a directory called DATA in the directory where you are storing your files (in the case of a thesis, have one such directory per chapter) and store the files there.

Keep only the latest versions of these files.