Reproduced, ticket opened here: https://github.com/bryntum/support/issues/79 Thank you for report.
As a workaround I would suggest to process updated records array and move them around checking ID.
As a workaround I would suggest to process updated records array and move them around checking ID.
const changes = gantt.project.getChangeSetPackage();
const updated = changed.dependencies.updated;
const added = updated.filter(r => /_generated/.test(r.id));
changes.dependencies.updated = updated.filter(r => added.includes(r))