Are there any cases where "prepend" cannot be replaced by "prefix"?

"Prepend" is seeing a fair amount of use, both in programmer jargon and elsewhere.
Its use seems to come from a desire to create a word that is a direct parallel to "append."

However, such a word already exists in "prefix."

They seem to need to be used differently:

To dial an outside line, prepend a 9 to your number.

versus

To dial an outside line, prefix the number with 9.

Are there any cases where "prefix" cannot be used in place of "prepend"? Any other insights into this word and its origins?

I'd say that the main reason that prepend is used is that it "sounds" like the reverse of append. According to Code Complete, you should have "opposites" for each method on an object, and they should "sound opposite". That's about it. Think of it like the British having to use American English while programming - they do it just because it's an established convention.

About "cases where prepend cannot be replaced by prefix": There are none, but as I said, it's a matter of convention.

To prepend means (as reported from the NOAD):

• (jargon, computing) to prefix an expression with another.
• (rare) to premeditate; to weigh up mentally.

The meaning of to prefix is:

• add something at the beginning as a prefix or introduction.
• add a prefix or introduction to something.

I searched for prepend in the Corpus of Contemporary American and the British National Corpus, but I didn't find any sentences containing that word. I think prepend is only used in a specific context, and that it cannot replace prefix in all the cases.

Aside from Aviral Dasgupta's answer, "prefix" feels like a noun (despite its etymology), so using it the way you suggest feels like an awkward verbing. It also suggests the usage of "suffix" as a verb, which feels like an even more awkward verbing.