What the heck does this mean?
You are confusing me.
"So I have a Flemish Giant female (pure, not inbred) and I have a New Zealand male (or at least that's what they told me, not inbred) and I bought that pair and bred them together twice."
Peeing blood doesn't sound good and if you can't afford a vet you can only do what you think is best.
If she appears to be suffering I wouldn't let her suffer if I were you.
If she's acting fine...don't ever give her the chance/option to get pregnant again.