The corrected version of the article says:
Mr O'Brien said any suggestion that the commission had revoked the organisation's charitable status was "simply false" and "misleading".
It is correct that the Commission notified Watchtower Australia (by the November 24 show cause notice) of concerns possibly warranting revocation of charitable status - namely that the organisation have not ensured its directors act in its best interests and failed to "take reasonable steps to ensure the safety of vulnerable individuals outside Australia" when donating overseas (nothing indicates the Commission questioned the very practice of sending funds to foreign entities); both issues involve insufficient paperwork, I guess. The November notice also asked Watchtower for comments, sent on 18 March.
The lawsuit is about preventing the ACNC from revoking Watchtower's charitable status; its subject is the proposed revocation decision.
Apparently, the Commission subsequently informed the org, either formally or informally, that it decided not to deregister Watchtower as a charity; once (and if) it is official, the court case becomes moot and will then be quickly withdrawn/dismissed.
The sources (the corrected article and the court application) are available here (not reader-friendly, though): https://youtu.be/OJeszWNAWOk