Safe Boot from the HD, (holding Shift key down at bootup), does the problem occur in Safe Mode?
Safe mode attempts to repair Disks & clears lots of caches, so if Safe Mode works try again in regular boot.
How to rebuild the Spotlight index on your Mac
If searching your Mac doesn’t return expected results, rebuilding the Spotlight index might help.
1. Choose Apple menu () > System Preferences, then click Spotlight.
2. Click the Privacy tab.
3. Drag the folder or disk that you want to index again to the list of locations that Spotlight is prevented from searching. Or click the Add (+) button and select the folder or disk to add.
To add an item to the Privacy tab, you must have ownership permissions for that item. To learn about permissions, choose Help from the Finder menu bar, then search for “permissions.”
4. From the same list of locations, select the folder or disk that you just added. Then click the Remove (–) button to remove it from the list.
5. Quit System Preferences. Spotlight will reindex the contents of the folder or disk.