Reading this, it looks as though they didn't run the checks. Usually in this situation I would expect the search to show up a pvn to prove that the business was doing the proper checks. It covers an employer if the time taken to do the checks for renewal of an evisa takes the applicant outside of the evisa renewal period. Hope that makes sense.
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If the business had run a check whilst the indefinite leave to remain was being processed, they would have been given the pvn to protect themselves from prosecution. They have been successfully prosecuted.
Regardless of the outcome of the employers rtw status, it looks as though this business didn't follow the law.