Are your sick leaves justified with a medical certificate from a doctor? Did you follow the protocol for applying for sick leave under your employee handbook?
It is presumed that an employee is apprised of the rules and regulations of the company he works with after receiving the employee handbook, especially if the contents of such were already explained by HR officers or any other administrators of similar duty. Furthermore, an employee has all the right to ask his superiors or HR department for any provision indicated in the handbook that he is confused with for further clarification.
As for the leave credits, if such provisions are explained and included in the employee's handbook, then it is presumed that you are knowledgeable of such. Due diligence dictates that you should have followed up your situation with your previous employer, especially since you needed to secure a Certificate of Employment for future reference.
Clarify everything first with your previous employer, and ask if there is any other recourse you could do in order for you to get your COE. You may have to pay the P7000 you owe the company for you to acquire said COE (maybe paying it under installment basis), unless you have compelling proof that the HR's basis lacks any merit.