Pycharm - Highlighting Non-Existant or Old Errors (especially when using jupyter on the side)

I have this frustrating issue with Pycharm where it seems to stop reading my code or updates and assumes there are many errors based on old code. For example, in the screenshot I attached below, my code runs fine. Even though we have many different false errors highlighted. Its also showing a duplicate code fragment that does not exist. 

I noticed this usually happens when I am also running Jupyter notebooks. My ram/cpu/disk is not maxed out so I am not sure what is happening. Any tips for improving performance or troubleshooting? This is an issue I have had for a couple months now.