The notes to the Aqdas say:

Shoghi Effendi, in letters written on his behalf, has
explained the significance of the "letters B and E". They
constitute the word "Be", which, he states, "means the
creative Power of God Who through His command causes
all things to come into being" and "the power of the
Manifestation of God, His great spiritual creative force".
The imperative "Be" in the original Arabic is the word
"kun", consisting of the two letters "kaf" and "nun". They
have been translated by Shoghi Effendi in the above
manner. This word has been used in the Qur'án as God's
bidding calling creation into being. (note 188)

I haven't been able to find the letters on behalf of Shoghi Effendi that are referred to here, either in the Persian or the English literature, and my search didn't turn up an explanation from Abdu'l-Baha either. 

Adib Taherzadeh in his book "The Revelation of Baha'u'llah v 1" explains it this way: 

"The Word of God is the noblest form of the creation of God and it stands far above the comprehension of man. Bahá'u'lláh has warned us in a Tablet never to compare the creation of the 'Word' with the creation of other things. He states that each one of the words of God is like a mirror through which the attributes of God are reflected, and that through the Word of God all creation has come into being. In Islam it is stated that God created the universe through the utterance of one word 'Be', which brought into existence all created things. The Revelation of Bahá'u'lláh which is the Word of God for this age is, in like manner, creative. Bahá'u'lláh has, in some of His Tablets, referred to the word 'Be' as the cause of creation. For instance, in the Tablet of Visitation which was compiled after His ascension,[1] He says: 'I testify, moreover, that with but a movement of Thy Pen Thine injunction "Be Thou" hath been enforced, and God's hidden Secret hath been divulged, and all created things have been called into being, and all the Revelations have been sent down.' Another example is the following passage in the Long Obligatory Prayer revealed by Bahá'u'lláh: '...He Who hath been manifested is the Hidden Mystery, the Treasured Symbol, through Whom the letters B and E (Be) have been joined and knit together.'(4) When the letters B and E are joined together, they make the word 'Be' which calls creation into being."

 (Adib Taherzadeh, The Revelation of Baha'u'llah v 1, p. 30)

What does "kun ma'Alláh" mean? What is its significance? Where is it written?