It depends on where that value comes from. If it was caused by incompatibility between scripts from mods or the vanilla game, the same bug may occur again, and since the parameters are hard to identify, it could become increasingly hard to mend, meaning you might have to readjust constantly.
Also keep in mind that
SetAV is targeting the base value of your character's attribute directly. Are you sure that particular value (as it can be seen in your Skills menu) is erroneous?
Moreover, according to the Wiki page, "some values reset after ending game". I don't know if this applies to the Magicka base value.
I suggest you look into finding conflicts between mods, and how to resolve them properly.
- This video gives a quick overview on how to do so with TES5Edit. If you prefer reading about it, you might want to use this guide.
- A more basic option is ModOrganizer, but it gives you less flexibility. I don't think you can actually consolidate conflicting scripts, so this could be useless, unless re-ordering mods can solve your issue. Here's a video introduction by the soothing and thorough Gopher.
- And then there is WryeBash, which is probably the most allround modding tool you will need, but its learning curve is steeper that the other two. You can use this page as reference.