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Jonah typically emerged from his office a handful of times during his scheduled workday. On his two fifteen-minute-long mandatory breaks and his thirty-minute lunch and if he happened to need to go to the bathroom or get a snack outside of those breaks. 

Back when Troy worked at Freddie's, he was home for part of this time depending on the day of the week. Eden never was because her work hours were roughly the same as his. 

So when she called in sick just because she wasn't in the right headspace to deal with Zim (and, honestly, he couldn't blame her with all the stories he had heard) he came out multiple times throughout the day to find her moping on the couch. Each time, he found her watching a different chick flick.