It's not silent, but phonetically it's more like a soft -d sound and quite subtle :)
"subtle" is one way of putting it. To me it's totally inaudible, even on slow!
"I did not eat the sugar" is "Jeg spiste ikke sukkeret". Spiste is the past tense of spiser (which is present tense).
"Jeg" is pronouncing different in sentence than on its own. A little bit confusing.
I think that only way to know to use sukkeret instead of sukker is to look at the other words in the sentence and see how it sounds in english as a whole? Does 'I am not eating sugar' sound wrong? Not to me. But I got marked wrong for using sukker. Unlike Swedish, the silent -et at the end will be a challenge for learning Danish.