If the absence is due to illness, regardless of whether it was employer initiated, then the employee will need to produce a medical certificate, then the employer must use accrued sick leave first. If the R&R leave (i assume accrued similar to TOIL) has not been documented it will be problematic, but if the employee decides to pursue compensation for it then all they need to do is demonstrate that they had worked it, which is easier to do than the employer trying to demonstrate that they didn't.
Do you have a enterprise agreement in place? If so what does it say?
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