The amnio test is normally over 99% accurate, but results can be affected as the pregnancy proceeds. The later the test is done, the higher the chances of maternal contamination affecting the results. She did have it done fairly early, so this is less likely, which means the test has more likelihood of being accurate. Has the lab been contacted as to why the second test results have not yet been reported? It may just be an omission by the lab, or a judgment that since the first test showed only one thal gene, that it may not be necessary. For your own peace of mind, you should get an answer to this. Have your doctor contact the lab and find out if these results will also be given. Your deletion is one that is routinely found in testing, so it's unlikely it would be missed. Unless your report said something specific about the level of maternal contamination affecting the test, you should have nothing to worry about.
You both carry beta zero thal deletions. If a child was to inherit both, the child would be a thal major. Genetic counseling is recommended before attempting any future pregnancies.