StitchBuddy can only save Brother files in PES version 1.0, although higher versions can be read. These newer file versions are more sophisticated, holding enhanced data like thread charts and more.
If you overwrote such an enhanced file format with the simplier PES version 1.0, the additional information would be lost. This is the reason why e.g. a PES v2.0 design cannot be written under the same name.
TL;DR … just use the "Save as…" command to save changes of a higher PES version, resulting in a PES v1.0 files.
