'Des' is used to express the idea of 'some' and in positive sentences and most contexts, it remains as it is in the example sentence you used above,
"Y a-t-il des fleurs dans votre jardin?"
"Are there [any/some] flowers in your garden?".
When the sentence appears in the negative form, then we switch to 'de'.
"In n'y a pas de fleurs dans mon jardin."
"There are no flowers in my garden."
Perhaps it is best to think of it in the same way as in the English version where we exchange 'any/some' in the first sentence, to 'no' in the second, negative sentence. There are also other fixed phrases such as, 'beaucoup de' where the 'de' never changes, regardless of what follows it.
I hope this helps,