Interesting. Could you determine if such a program had been used to make the modifications?
There are several dates in the metadata of the file. You would probably want to check them all. You might catch an anomaly.
Look for inconsistencies. It’s all files. All stamps the same date time? Examine contents for date,references that don’t jibe. What kind of files? .jsp and htm files have all kinds of meta data. Even word processing documents and pdfs have internal meta data.