If you mean the KSE one, I think it's called, then no, there's no major issues with it that I've seen, as long as you stick with modifying simple things. I haven't messed with the feats and stuff tho...just the influence, NPC experience (I hate that they fall behind....grrrr), and occasionally adding items for tinkering/screenshot purposes.
Just save a game in a new slot and edit that file, you'll still have the original unedited savegame if something goes wrong.