Let me try and explain: Your post is a bit confusing because you wrote above "I have included my wife on the my I-485 petition and also applied for advance paroles for both of us." But later you wrote "She doesnt have an AP yet. I will file for her."
Please note (and I assume you know this already but am repeating for clarity):
1- I-485 is not a petition, it is an application.
2- Before you are eligible to submit an I-485 application, you must have an approved or submitted Immigrant Petition, such as an I-140, or you must file both together if you are qualified (non-retrogressed country).
3- You can file a petition for yourself, but you must file a separate I-485 application for each member of your family. Each I-485 application must include a medical exam, G325A biographic information sheets, and other evidence.
Please answer:
1- Did you send an I-485 application for yourself?
Yes
2- Did you send a separate I-485 application for your wife?
Yes
3- Did you, or will you, submit a I-131 Advanced Parole application for each of you?
Yes
To answer your question: The status your wife is given at the point of entry is the status she will be under in the United States. If your wife leaves the US as a J-1 but reenters as a parolee (which at this point is the only way she can enter because she is ineligible to apply for a new J-1 visa abroad since she filed for adjustment of status), she will NOT be able to continue her J-1 status upon reentry. Therefore, take mmed's advice and apply for an EAD also. If she doesn't have an EAD when she comes back as a parolee, she cannot work anymore.
However, if you are in valid H-1B status, your wife CAN apply for an H-4 visa abroad and return to the US on an H-4. But she will not be able to work on the H-4, so she will still need an EAD. She can apply for the EAD (I-765) along with her I-485 application. She cannot apply for an EAD before she applies for the I-485 application.