What happens if you modify the file after the deposit?

If you modify the file after depositing it, even by a single byte, its fingerprint changes entirely and no longer matches the issued certificate.

This is precisely what makes the method useful: the certificate attests to an exact state of the file at a given moment, and any later divergence is immediately detectable during verification.

For a new version of a file, the process is simple: make a new deposit. Each meaningful version of your work can thus have its own timestamped certificate.