You can send the reject flow to a tMap and build an output flow for the rejected records with the same schema like the original input component. To do that connect the reject flow to a tMap. Add to your job and tFileOutputDelimited (for the rejected records) and the as schema the schema of the tFileInputDelimited (origin of your data) by copy and paste the columns in the schema editors.
Now connect the tMap with the new tFileOutputDelimited and accept the target schema for this flow.
Within the tMap you can adapt the reject flow schema to the new output.