I just want to point out that I am not a lawyer, but you are. Ha! Actually, I write this to demonstrate that should somebody else need legal advice in an employment situation, it's important to find someone who practices employment law, as clearly not all lawyers can address all situations. (This, of course, is true for everything. You don't want a criminal lawyer handling your merger either.)
First the lecture: How could you not know until she went out that there were problems? Not saying that things can't be hidden from managers, but when you wait until the person is out on maternity leave, it looks awfully suspicious. In fact, as a lawyer, you know that this looks suspicious, which is why you are asking.
Now, the instructions. Document as you would if she were still working. Keep to the strict policies that (I hope!) you already have in place. Make sure you don't hold her time off against her. I presume she's not eligible for FMLA because you are a small firm, but if she is, remember that any time off for FMLA can't be considered in performance appraisals and similar.
You need to treat this exactly the same way you would treat it if she were still in the office--with the exception of actually calling her up and saying anything. That will not go over well and even if she knows it is all true (which she may not, denial runs deep in the bad employee world), she will take this as a sign that you want to fire her for having the audacity to have a baby.
When she returns from maternity leave, you welcome her back and look at all the pictures of her darling little baby. (And hope to heck the baby is darling--there are some ugly ones out there and gosh it's hard to be polite when a picture of a little troll is shoved under your nose.)
Then, invite her into your office and explain what you've learned and how it is a problem and work with her to develop a plan to avoid this in the future. The key point here is that you must treat her exactly the same as you would treat anybody who didn't just have a baby. Best way to cover your behind is to treat everyone the same.
Now, this all assumes that what she's done wrong is not a fireable offense. (Note to picky people--I realize you don't need a reason to fire someone in the US, but most companies don't generally fire people just because. Besides, that's not nice.) If this is a fireable offense you need to fire her, but only if you would have fired someone else for the same thing.
Now, I know it's sticky because of the whole baby thing. This is why I like frequent performance reviews and one-one communication because you don't want things like this getting out of hand and having no one know anything until suddenly the person is in a protected class. Like, you don't want to be quiet and hope that a situation gets better and five minutes before you planned to finally discuss it--after 6 months of worsening behavior--have your employee announce she's pregnant, gay, born-again-Christian, Pagan, or something else. You know the reason you're having the discussion is the bad work behavior; the employee sees it as discrimination against whatever she is/was/will become.
Being a manager is tough. That's why managers get paid more.