I'm happy to give you some advice here. From your description, you think that something is wrong with Spotlight indexing, leading to the files/folders on the external disk disappearing from time to time in Mac Finder. In fact, the first thing you need to take into consideration is whether it is caused by loose or faulty connections.
Are you using any adapters or USB hubs to connect the external drive to your MBP? If so, try to remove the USB hub and directly connect your external disk to your Mac or change to another adapter. If you don't use the adapter and USB hub but directly connect your external drive to MBP, try another port.
If the issue continues, try to check if the Spotlight Search indexing problem makes the trouble. You can rebuild the Spotlight indexing with these steps:
- Open the Apple menu > System Preferences >Spotlight > Privacy.
- Click the add (+) button on the window to add the content that the Spotlight failed to locate (that is the content on your external disk).
Still, nothing changes? Try the tricks below to fix the files not showing up on Mac external hard drive issue:
1. Boot your Mac in Safe Mode to verify if the randomly disappeared files on the external disk are caused by third-party conflicts or not.
2. Run Disk Utility First Aid to repair the disk. The missing files/folders on the external disk may be also due to file system errors. First Aid can check and fix tiny errors on the external disk.
If files on your external disk are completely disappeared, you can refer to this guide: Recover Files Disappeared from External Hard Drive on Mac.
