Is this legal? Does that mean in anyway that it can also be enforced for agreements in the past?
This is hard to answer because your description is somewhat confusing. The first paragraph is unclear as to whether the benefit at no-cost is contingent only on the employee's completion of the course prior to leaving the organization, or also on the employee being employed for at least a certain period (regardless of the duration or completion of the course). For simplicity, I'll assume the former scenario. Also I'll assume that the benefit the organization provides is a course, not a policy.
A party cannot unilaterally alter a contract or agreement, at least where the change is detrimental to the counterparty. However, the disclaimer "this policy can be changed without notice" complicates the assessment. The issue depends on whether the employee's notice of resignation preceded the employer's change of terms.
On the one hand, the disclaimer is tantamount to what the Restatement (Second) of Contracts at § 154(b) labels as [employee] bearing the risk of mistake: The employee had limited knowledge of whether, when, or how the organization might change the policy, and yet the employee accepted the disclaimer.
On the other hand, the reliability of contracts is severely weakened if either (or both) party(-ies) is entitled to unilaterally modify conditions. The disclaimer as portrayed does not even clarify that only the organization may change the policy. Thus, the disclaimer seemingly entitles the employee to change the policy to the organization's detriment just as it entitles the organization to do so.
The disclaimer (again, as portrayed) is sloppy enough to render itself meaningless: Each time a party changes the policy, immediately thereafter the counterparty may change the new policy to the effect of restoring it to the original.
The analysis ought to focus on what conditions the employee reasonably could have pondered by the time he gave his notice of resignation. Otherwise, the disclaimer would give the organization carte blanche to even require full reimbursement of the course, regardless of duration of employment and regardless of how long ago the employee completed it.
Given that the employee agreed to the disclaimer, the conclusion that the organization's change of policy cannot be retroactive to the employee's notice of resignation is most consistent with the tenets of contract law.