I have a bunch of papers in my One drive, in folders that are synced to my hard drive, that don’t show up on the Window search (microscope icon). Is there some way to get those files indexed so I can find results easily.
Your desktop Search experience will depend on the version of Windows. But you can change your Windows search settings from Control Panel.
Personally, when searching on any cloud-stored content (OneDrive, DropBox etc) I find it's better to use the online search interface as it will typically index more file content, and the search is much faster.