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I think you are correct. The second run of the command would would likely change most the outputs to inputs in the .deps file. Assuming only a few files are rebuilt.
To fix that it may require some analysis of the old dependencies when a command is re-run. Original outputs should remain outputs even if they are just listed as inputs on the re-run.
Thinking about it there may be other cases where this is a problem. E.g. Re-run of command due to deps change produces an output file with a different name. The new dependencies will not include the original output file (which is correct) but the original output will not get cleaned. That may need a new type in the deps file 'old-output', which will get cleaned but not cause a re-run if it is changed or removed.
Simon.
Thinking about it there may be other cases where this is a problem. E.g. Re-run of command due to deps change produces an output file with a different name