Yes, as far as the mod you're working on goes, you should be fine. Where you might run into trouble is if you leave the mod you're working on active while you're playing the game as this will lead to various data about your "work in progress" mod being added to your saved game. If you then change, remove things from your WIP mod it might have an adverse affect on your saved game. This is particularly true for scripts that your WIP mod might the using. When it comes to testing your mod, it's generally recommended do that on a clean, un-modded skyrim.