There are numerous "studies" (sorry I can't cite them, but I've read this in many different mainstream publications) that say missing your period for a few months at a time every so often is NOT harmful. That's provided of course it's not due to something like anorexia and malnutrition, which could result in bone loss and other problems.
I've even read some studies saying that constant monthly menstruation for a long time without any interuption (such as pregnancy) is dangerous and can predispose a woman to certain types of cancers (e.g. breast) which are related to high estrogen.