This depends on a number of factors.
As per Maltese Tax, when an employee working with a Maltese based company does not reside in Malta for more than 6 months they are to pay the Non-Resident Tax Rates. This is a higher rate than the standard Single, Parent and Married rates.
Official CFR Non-Resident Tax Rates
Once the employee has resided in Malta for at least 6 months, the standard tax rates, equivalent to what you would use for a Maltese employee would come in-effect.
Should you opt to use resident tax rates for an employee you've just hired and has just moved to Malta, and the employee leaves before residing in Malta for at least 6 months, the CFR may try to recover the difference in taxes from the company, as that would be the entity that's left in Malta.
Should a person be taxed at non-resident rates, following 6 months this should be amended to a resident tax-rate. At which point tax for that calendar year will be automatically adjusted by Buddy.
Tax paid for previous calendar years, can be claimed following the receipt of the annual Tax Form, by requesting a change of status for the year.