Currently the WriteTables transform deletes the set of input files as soon as the load() job completes. However this is incorrect - if the task fails partially through deleting files (e.g. if the worker crashes), the task will be retried. If the write disposition is WRITE_TRUNCATE, bad things could result.
The resulting behavior will depend on what BQ does if one of input files is missing (because we had previously deleted it). In the best case, BQ will fail the load. In this case the step will keep failing until the runner finally fails the entire job. If however BQ ignores the missing file, the load will overwrite the previously-written table with the smaller set of files and the job will succeed. This is the worst-case scenario, as it will result in data loss.