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Do you need to convert the single sentence to a single sentence? If so, I would go with the approaches chosen by Tashus ("... where the cube represents" or "... with the cube representing...") or Utkarsh Singh (using "former" or "latter" to refer to the item in question). If you're not restricted to a single sentence, you can simply repeat the noun in a new sentence:

It's a sphere inside a cube. The cube represents a parent shape...

UPDATE: As David Richerby points out, you could then combine the sentences with a semicolon or a connecting word:

It's a sphere inside a cube; the cube represents a parent shape...

It's a sphere inside a cube, and the cube represents a parent shape...

It's a sphere inside a cube, where the cube represents a parent shape...

In my opinion, the usage of the determiner "which" herein will inevitably lead to ambiguity. One of the ways to avoid this, while still retaining the word "represents", can be to instead use a co-ordinating conjunction like "and" - It's a sphere inside a cube, and the former represents...(in case the subject is sphere).

The easiest way to disambiguate in speech (which is after all the only real language, to a first approximation) is simply to stress the word sphere and introduce a slightly longer pause before the next word. Orthographically, that would be represented as...

It's a sphere - inside a cube representing the "parent" shape

(Note that I've included "parent" in scare quotes because I don't exactly understand the usage in context. If OP knows his target audience will understand the expression, there's no need to call attention to the potentially problematic usage.)

In terms of the particular sentence you gave,

What's a child sphere? It's a sphere inside a cube, which represents a parent shape.

There's only one thing wrong with it: the comma. You want

What's a child sphere? It's a sphere inside a cube which represents a parent shape.

When parsing a sentence, the comma gives us an indication as to the sentence structure. In your sentence, the comma indicates that the clause "inside a cube" is complete and you're beginning a relative clause referring to the sphere. Commas also correspond to pauses in normal speech, so that may help (though the correspondence isn't perfect).

This doesn't mean that this is the right sentence to use; while it's (technically) unambiguous, someone who is not reading carefully is likely to read it wrong.

It's a sphere inside a cube that represents a parent shape. The
that clause only goes with the cube.

There's a market along the road that runs to town.

There is no ambiguity here at all.

It's a man in a *balloon that floats** on the water.

My advice is kill the which in this case.

"that represents a parent shape" is a restrictive clause modifying cube. It does not modify: sphere inside a cube, which is a noun plus a prepositional phrase.

• 
  restrictive clauses modify a noun. Not a noun and a preposition phrase as found in the OP's sentence.

Example of an unrestricted clause from the Oxford Dictionary [online] made into a restricted one.

clauses, restricted and unrestricted

It says: A restrictive relative clause provides essential information about the noun to which it refers.

• unrestricted: The items, which are believed to be family heirlooms, included a grandfather clock worth around £3,000.




• restricted: The items that are believed to be family heirlooms, included a grandfather clock worth around £3,000.

The lines in the painting that hangs on the North Wall are not straight.

The other sentence in the question using a restrictive clause:

It's a call expression inside a function that represents a parent call
expression.