A DDL file now speaks only for the schemas it contains
Until now every DDL upload was treated as your project’s complete source schema, so a one-schema export marked every table in all your other schemas as removed. An upload now covers only the schemas present in the file.
This applies to every client, including CLI versions older than 1.6 that cannot say otherwise. If a pipeline of yours signaled a dropped schema by leaving it out of the file, pass --complete on cassis schema push, or answer that the file is complete in the app, to keep detecting whole-schema drops.