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There words are used in the Qur-an, with a meaning akin to "forgive" but each with a different shade of meaning. Afa (here translated "forgive") means to forget, to obliterate from one's mind. Safaha (here translated "overlook") means to turn away from, to ignore, to treat a matter as if it did not affect one. Gafara (which does not occur in this verse) means to cover up something as God does to our sins with His grace; this word is particularly appropriate in God's attribute of Gaffar, the One who forgives again and again.
The word Amr is comprehensive and includes (1) an order or command as in xcvi. 12; or (2) a purpose, design, will as in xviii. 82; or (3) affairs, working, doing, carrying out or execution of a design, as in lxxxix 5. In many cases some of these meanings run together.
Note how this phrase, seemingly repeated from ii. 106, and occurring in many other places, has an appropriate signification in each place. In ii. 106 we were told about progressive revelation, how the same thing may take different forms and seeming human infirmity contribute to the fulfillment of God's design, for God's power is unlimited. Here we are told to be patient and forgiving against envy and injustice: this too may be fulfilling God's purpose, for His power is infinite.