Append simply means "add to" or "attach to"; it's not restricted to adding something to the end of or after something else. An antonym for "append" would therefore be words such as "remove" or " detach, or any word that means "take away from".
"Prepend" is jargon invented by computer programmers who have possibly misunderstood the meaning of "append" and are not aware of the words "prefix" and "suffix", both of which can be used as verbs. As a computer programmer
and language pedant, I am forever correcting people on that one!