No, deleting lessons won't affect your Known words count or LingQs created.

This is a comment from Mark (the CEO) in another thread: "The lesson is removed but LingQs and word data is retained. Why would you want to delete your LingQs? The idea behind our word tracking system is that it tracks all words you encounter and identifies whether words are known, ignored or being learned (LingQs). Whether you delete the originating content or not doesn't change your relationship with those words. If the LingQs you created in that deleted content matter, they will reappear in future lessons. If not, they will remain forever unlearned, no harm done."