My sister’s husband has been absent since 10 May 2000. We do not know his whereabouts until today, so we filed for divorce. In January 2006, the court granted my sister a divorce. When will her ‘iddah waiting period after her divorce be?

If the case is as mentioned in the question, then the ‘iddah of the divorced woman (the inquirer’s sister) will be from the date she was granted the divorce (January 2006); it is not from the date of the husband’s absence.
And Allah knows best.