I assume the child will be returning after the birth, after the vacation time is used? Or does the birth act as their end date?
If the child is returning, then if they have already paid they have already paid. Just note when payments are and when the child is away, then when they return use up the remaining paid days and unpaid vacation days before next payment is made.
As much as it is kind to allow them to use this time for the birth of their child it is way to much work to be refunding money at random when the child finally does arrive. Just make note of what paid days remain and subtract those days from next payment to balance it out.
Do let them know that since the lack of firm date complicates matters you will use the above plan and lay it out so their are no surprises.