Depends on the circumstances.
Who requested the evaluation? Who chose the evaluator? Was it court ordered? Is there any obvious bias? Was there factual information that the evaluator did not consider in making his report?
In general, courts like to put a lot of emphasis on custody evaluations, especially when there's no reason to think that it's unfair (such as when both parents are involved in choosing the evaluator). Basically, the presumption is that CEs are trained to evaluate what's best for the kids but judges are not, so many (not all) judges prefer for the 'expert' to make an evaluation.
Then, a lot depends on what 'she is not doing what she should on her part' means. If the kids are currently doing well in school, well clothed, well fed, and the CE says they should stay with the mother, you're going to have an uphill battle unless you have something you're not disclosing - particularly related to the above questions.
In my case, we had an agreement for 50:50 parenting. We have been alternating weeks for the 5 months we've been apart and my daughter is thriving. My stbx changed her mind after seeing my financial settlement offer and demanded a custody evaluation. She and her attorney gave us 3 names and we selected one of those 3. The evaluation said that we should leave things the way they are. Both my attorney and Soc said that it would require some very major blunder on the CE's part to make the judge ignore that recommendation.