Hi, I'd like to help you with your question.
It is very common for couples who are trying to work on their marriage to experience ups and downs as they work through the problems that cause the separation.
There are several reasons for a couple to separate. One is for a divorce, which in your case is on hold and not a priority, to gain perspective on the marriage so you can work out problems, and to help your marriage improve.
Sometimes being apart can make you appreciate each other more. It seems to have helped your marriage in that you are now having good days together and your wife has put the divorce on hold. That means that she has hope that the marriage can be repaired. But along with that hope, she also has doubts. These doubts can come up at any time, but may especially come about when she is feeling good about the relationship. This can cause her to back off and need time to think things through.
Added to the doubt is your wife's recovery. If she is in AA, then I assume drinking was an issue at some time for her. Past alcohol use and current treatment can cause her moods to fluctuate and make recovery more difficult. The stress of the marriage problems can also add to her desire to use again. She may need time to gain control again of her cravings after she is with you.
It sounds like you are doing a great job in working on your marriage. Keep doing what you are doing. Ask your wife if there is anything else she needs from you emotionally or otherwise. She can tell you if there is something she is concerned about. Communication between you is the most important factor in working your marriage problems out. You are doing all you can to be there and change things to improve your marriage. It is up to her to do her part as well. Time and patience are the best things to give her.
I hope this helps you,