You don't need the letter to complete the quest.
The letter is delivered to you only if you were below level 15 when you hit a certain point in Discerning the Transmundane, then leveled up past that point. It just tells you you're a high enough level to return to Septimus Signus and continue the quest.
To continue past this point, you must be level 15 or higher. If you aren't level 15 yet, giving Septimus the Lexicon will result in him dismissing you; then, you must wait until a courier delivers a letter from him to continue.
According to the discussion page for the letter itself, you will get a quest marker by reading the letter. However, you should be able to return to Septimus Signus' Outpost and continue the quest without it.