1. That's the part I'm confused about tbh. I forgot the explanation. I'm not sure if it's that they looked similar or some sort of face swap?? I'd need to reread but there like 600 chapters...
2. Yan Zhe has not been introduced in the show yet, but he's one of Yan Chi's cousins, who is also a prince. His mother helped Yan Han, the imposter king, a long time ago, and he used a poison on her that she could not detect fast enough; his mother was a doctor, so she died. He also used the same poison to make Yan Zhe go blind. His character will be introduced soon. He's behind a lot of the things going on in the capital because he's trying to get revenge on Yan Han for killing his mother.
3. Yan Han goes after Yan Chi's dad and their family due to their military power, so Yan Chi and Qin Wan are forced to flee, thus declaring them and their army/followers rebels. He fights some wars, and he/Qin Wan aids the empress, who was also declared a rebel. The empress gets shot with an arrow and her health declines, so the soldiers who were under her and her father decided to help Yan Chi and Qin Wan with their cause. Yan Chi and this new group go to the capital and demand that Yan Han give up the throne due to his misdeeds, and Yan Zhe aids them by slowly poisoning Yan Han. There's more to the story than this, but it would take me forever to type.
4. Yan Li and his mom have a bad rep in the capital due to everything that has happened, and despite YC/QW's love and protection for them, they decided that they wanted to travel and get a fresh start. So they leave the capital. It's unknown when or if they will return or not.
5. I forgot the specifics on what happened to YN tbh. But she and YL aren't a couple in the novel, so...yeah. I don't remember anything bad happening to her. The last thing I remember is her considering who she should marry. I'm almost certain she had a happy ending, though.
6. Yan Zhe had Li Mu Yun submit a memorial to expose the Shen family, which is why Shen Yi died. He wanted to use their family to test the emperor, and also because Shen Yi and Prince Jin learned about the emperor's secret, which is that he's not the real emperor.
Here are some short passages from chapter 441:
"Seeing Yan Chi’s impassiveness, disappointment arose in Yan Ze’s eyes. His lips pressed slightly as he said, “The late Emperor passed the throne to Prince Luo, but His Majesty has been an impostor for many years. The Shen clan you mentioned, and the Jin Prince, even Jin Consort—they were all merely sacrifices to his ambition. From this, we can see that the royal bloodline must return to its rightful succession. Initially, I thought with the current Crown Prince firmly seated as heir apparent, he would surely inherit the throne, thus returning to the proper way. But now you know—His Majesty has no intention of letting the Crown Prince inherit the throne. All of Prince Luo’s descendants are merely his pawns to deceive people…” "
"Yan Ze’s phoenix eyes narrowed slightly. “You’re still too soft-hearted, Yan Chi. When Mother Consort and Aunt Princess died one after another, it was all because Mother Consort learned His Majesty’s secret while treating his illness, and then… Perhaps I don’t have your self-control. Now, I’ve decided to pull out the firewood from under the cauldron and fight with my back against the water. But you still have a way out—you have one hundred thousand Shuo Xi troops waiting for you. Once you reach Shuo Xi, you can leave behind all the grudges of the capital.” "
So in short, yes, that's why the little prince is afraid of his dad.