It's not me, but someone else. Anyway, the person has been living in Nepal but being paid as an employee from a Thai company. I don't think income tax can be paid in Thailand as I understand you need a visa, Thai address, etc for that. Which leads me to assume that no tax would have been paid, and the person should instead be subject to a withholding tax deduction from their salary. All very complicated I know.
But, if they are treated as a consultant for tax purposes can they then still be an employee?