Notes main folders will not stay collapsed.

This issue was occurred for some users on macOS 26 Tahoe, as well, and was due to a corrupted preference file. If your folders are expanding even when you haven't fully quit the app, it may be a corrupted preference file.

You can reset it by following these steps:

• Close Apple Notes.
• In Finder, select Go menu > Go to Folder and paste the following, then press return

~/Library/Containers/com.apple.Notes/Data/Library/Preferences/

• Locate com.apple.Notes.plist and move it to your Desktop.
• Restart your Mac and open Notes. If the behavior stabilizes, you can delete the file from your Desktop.

If you don't want to go that route, you can use a keyboard to collapse the folders.

Keyboard Shortcuts for Quick Collapsing

If you just want an easy way to clean up the mess when you open the app without hunting down folders manually, use this built-in navigation trick:

• Click inside your sidebar folder list, press Command + A to Select All, and then hit the Left Arrow key.
• Alternatively, holding the Option key while clicking a top-level arrow will collapse or expand all subfolders nested beneath it instantly. 

More info from Apple: Keyboard shortcuts and gestures in Notes on Mac - Apple Support