According to the IRS Section 125 document (clicking the link will download a PDF, then see paragraph c, which starts on page 15) the birth of a child is a "qualifying life event". Pregnancy does not entitle you to increase the total amount you contribute to your FSA, but you seem to know that.
Maybe I missed something, but I've not found any IRS rules about increasing contributions now to compensate for a lack of contributions later in the year. That said, my experience is that FSA contribution amounts per paycheck are locked in when the employee finalizes their election prior to the start of the plan year (unless one of those life changing events occurs). However, since I didn't find a regulation to that effect, it may be possible to make such a change.
You suggested using paid time off to continue making contributions if it's not possible to increase them before unpaid time off. That should work if the employee has sufficient PTO to cover their time off. If they don't have that much PTO here are a couple other suggestions - unfortunately I don't know if these are permitted with FSA's:
- They may be able to use an amount of PTO less than their regular workload to keep making FSA contributions.
- The employee may be allowed to make out-of-pocket contributions (i.e. they directly pay into their FSA fund) during that unpaid time.
Generally speaking, the FSA plan administrator (either internally or at the agency providing the benefit) should be able to provide more help.