When Elizabeth Malcolm nee Cugley married Otto Koeller she stated she was a widow, her husband having died in April 1888. There is no record that I can find for a death of Thomas Malcolm around this time period.
It must be taken into consideration that Elizabeth, at the time of her marriage to Otto, was living with her widowed mother. Elizabeth was a mother with four young children and no means of support and so a second marriage was a preferable option to her. It was probable that she had no idea where Thomas was and so claiming that he was dead was expedient when she wished to marry Otto.
I believe the last trace I can find for Thomas was the 1901 Electoral Roll where he was living at Mountain Run, Macquarie subdivision. There was also a James Malcolm at the same place. This was gold mining country and both Thomas and James were gold miners in Daylesford and James died at Mareeba from miners Phthisis.
As Thomas Snrs D/C states that both Thomas and James were still living in 1911, I am willing to accept this. James was certainly alive so it is not unreasonable to also acccept that Thomas was also alive.