Going by your statements, it looks like you do have very stable employees; otherwise, this situation wouldn't have arisen. I don't think there's anything to feel bad about introducing a short-sighted policy as long as you are willing to learn and correct along the way. Many companies fail in this crucial aspect.
Query/Concern
Please confirm the domain/sector your company is in—IT, Telecom, etc. Since you are in the Philippines, I suggest evaluating the general Leave Policies in other similar-sized companies in the same sector. This would give you some semblance of being on par with industry standards and ensure your employees don't resist whatever changes you bring about.
Steps to Fix the Situation
As for how to fix the situation, I suggest first consolidating the pending leave dues of each employee into a fixed leave balance, rounding off to the nearest numeral as of the current date. You could retain the leave balance as it is or maybe pay the employees a fixed amount for the leaves you wish to be 'abdicated' or lapsed.
Then introduce the new leave policy, which will take effect from a predetermined date that you need to inform the employees in advance. With some fine-tuning, you should be able to get a model that will be, by and large, acceptable to all—and more importantly, that would stand from the long-term standard viewpoint.
All the Best.
Regards, TS