The Latin prefix « re- » does not mean the preposition (and not particle) 'up' in 'break up':
so what semantic notions underlie « re- » with 'up'?
The only way I could see re- meaning "back" is that breaking something is undoing its construction. But a corpus search quickly suggests that this is not implied in a typical use of the verb.
Instead, re- is simply an intensifier here.
A Latin prefix may nominally indicate some kind of location, but you cannot generally reduce the meaning of a prefixed verb to the meanings of the verb and the prefix. For example, invenire aliquid does not really mean venire in aliquid, unless you stretch it quite a bit. Prefixed Latin verbs are like phrasal verbs in English. For example, I can "write up" or "write down", but it has no effect on the direction or location of my text. Or more related to the verb at hand, you can "break up" or "break down", but again no direction is implied.
Sometimes a Latin prefix has its obvious meaning, but you cannot rely on that.