Filing I-485 While I-539 Pending

My mom is visiting us in the US. Her I-94 expired on Nov 20, 2008. However, prior to its expiration we filed I-539 asking for an extension till the end of December hoping that she can spend Christmas with us. We haven't gotten the reply yet, but she was planning to leave at the end of December regardless as we might not hear back from CIS for a while (btw, would it mean that application was abandoned?).
At the mean time I had my citizenship interview and my case was approved. Does it make sence to apply for AOS concurrently with my petition I-130. Our concern is: can we file I-485 while I-539 is pending? Will it affect decision on my petition and approval of I-485?
If she returns home and does application thru Consulate, will they question her stay her for over 6 months?
Thank you

You're talking about filing an I-130 for the benefit of your mother, after you become a citizen? Based upon the skeletal facts, I would suggest that you petition while she's in her home country; the I-539 is deemed abandoned if she leaves, but she would ordinarily be considered to be in legal status while the I-539 is pending.

Consider running the details of your situation past an immigration lawyer.