Hi rudolph210,
Thanks for posting your question. I understand you might be having an issue with Finder sidebar preferences.
To double-check, are you saying that you need to re-check the "External disks" box under Finder > Preferences > Sidebar each morning? Or are you referring to specific folders that you're adding to the Favorites column in Finder?
Are you powering your Mac off at night, or is it in Sleep?
Is your external hard drive connected to the computer overnight? It could be helpful to uncheck "Put hard disks to sleep when possible" under System Preferences > Energy Saver, and then keep an eye on it to see if that makes a difference: Use the Energy Saver settings on your Mac
As another test, if you add a folder from your internal hard drive to the Favorites column, is that one retained?
Which macOS version are you using under Apple menu () > About This Mac?
I hope this helps get you started.
Take care.