Well, since magnesium effects both calcium and alkalinity - causing swings in alkalinity could cause your pH to also swing way out of balance which could kill a major population of bacteria which can cause ammonia spikes which would kill your fish and corals. Magnesium is very important in a reef aquarium to maintain levels between 1300 and 1350mg/L
I suggest using some magnesium sulfate to bring your magnesium levels up. You can buy it pretty cheaply at your local drug store. They sell it as epsom salt. Look up Randy Holmes-Farley's 2 part recipe... it will tell you how to make it. To my knowledge, you dissolve 4 pounds (one container) of it into 1 gallon of ro/di water. I believe 4oz brings magnesium up by 50ppm in 25g of water. Check me on that though.
Magnesium chloride is also found in natural sea water. If you want to really get technical, you're supposed to mix roughly one pound of magnesium chloride to two pounds of magnesium sulfate - but to my knowledge they don't just sell magnesium chloride in a cheap form... I haven't been able to find it cheaply where I live. I know up north they sell it as "mag flake" which I *think* is some kind of road de-icer. Again, make sure you confirm all of this before doing it.