Microwaves change the molecular structure of foods. The process is called “cooking.”
All cooking methods cause chemical and molecular changes in our foods. A cooked egg certainly has a different chemical composition from a raw one.
No method of cooking will destroy minerals. But heat will destroy vitamin C, for example, no matter how the food is cooked.
Because microwave heating is uneven, parts of the food may be subjected to much higher temperatures than in other methods, so there is the possibility of some vitamin destruction.
But even if microwaves destroyed all of the vitamin X in your dish, there certainly wouldn’t be any nutritional harm in eating an occasional dish that doesn’t contain vitamin X. In a balanced diet, every dish doesn’t have to contain every vitamin and mineral.