Is it permissible to say, "Yes, I missed you" to someone you do not actually miss at the present moment, intending that you missed them at a previous time? Is this considered a forbidden lie? And what should be done to avoid lying and not harm a Muslim?

It appears there is no harm in using ma'areed (allusions/double entendres) when there is a need or for the sake of courtesy, as they do not constitute lying. Ma'areed means that the speech has an apparent meaning and another hidden meaning intended by the speaker. They are permissible and provide a way out of lying.