@Tikaania For the flickering, try enabling vertical sync, either in-game or through the control software that comes with your graphics driver. The in-game option is with the other graphics settings. You need to be in fullscreen mode for v-sync to work.
If that doesn't help, please run a dxdiag and attach it to a post.
https://help.ea.com/en-us/help/pc/how-to-gather-dxdiag-information/
For the other issues, did you try replacing the study door, or turning it to face the other direction? Which way is the front door facing, and will visiting sims use it if you temporarily remove the side door?
Cheats can cause problems, especially the MoveObjects cheat, but you should be able to fix that at least by disabling the cheat and then moving or replacing all affected items. It might take some time and effort though.
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