Disappearing Folder/Files

Do you have any backups?

What else is going on with the system? Are you running any other apps that may clean up or alter the OS with background jobs?

Obviously files & folders should not just disappear, what you describe is similar to what can happen during a large deletion (possibly initiated via Terminal) - files exist until they get processed at which point they are gone from spotlight & they never go into the Trash.

I would be very concerned that other items will be disappearing too. Reboot the system at the very least to stop any errant processes that you may have initiated. I would consider running under safe mode to prevent any background jobs continuing to run (hold shift at startup). The OS will be slower under safe mode, but at least you can be sure that something is not going to delete more files.

Try safe mode if your Mac doesn't finish starting up - Apple Support

If you have no backups use safe mode to create one ASAP or ask how to do so in recovery mode.

I guess it could also be due to disk damage, in which case check the disk via Disk Utility in Recovery mode (hold cmd+r at startup).

Run the verify & repair action of the first aid tab for the boot disk & the entire disk (the physical disk is listed above the boot partition). Make a note of errors listed - please ignore the errors listed in the permissions repair - they are not critical.

Back up all data before proceeding.

This procedure will unlock all your user files (not system files) and reset their ownership, permissions, and access controls to the default. If you've intentionally set special values for those attributes on any of your files, they will be reverted. In that case, either stop here, or be prepared to recreate the settings if necessary. Do so only after verifying that those settings didn't cause the problem. If none of this is meaningful to you, you don't need to worry about it, but you do need to follow the instructions below.

Step 1

If you have more than one user, and the one in question is not an administrator, then go to Step 2.

Triple-click anywhere in the following line on this page to select it:

sudo find ~ $TMPDIR.. -exec chflags -h nouchg,nouappnd,noschg,nosappnd {} + -exec chown -h $UID {} + -exec chmod +rw {} + -exec chmod -h -N {} + -type d -exec chmod -h +x {} + 2>&-

Copy the selected text to the Clipboard by pressing the key combination command-C.

Launch the built-in Terminal application in any of the following ways:

☞ Enter the first few letters of its name into a Spotlight search. Select it in the results (it should be at the top.)

☞ In the Finder, select Go ▹ Utilities from the menu bar, or press the key combination shift-command-U. The application is in the folder that opens.

☞ Open LaunchPad and start typing the name.

Paste into the Terminal window by pressing command-V. I've tested these instructions only with the Safari web browser. If you use another browser, you may have to press the return key after pasting.

You'll be prompted for your login password, which won't be displayed when you type it. Type carefully and then press return. You may get a one-time warning to be careful. If you don’t have a login password, you’ll need to set one before you can run the command. If you see a message that your username "is not in the sudoers file," then you're not logged in as an administrator.

The command may take several minutes to run, depending on how many files you have. Wait for a new line ending in a dollar sign ($) to appear, then quit Terminal.

Step 2 (optional)

Take this step only if you have trouble with Step 1, if you prefer not to take it, or if it doesn't solve the problem.

Start up in Recovery mode. When the OS X Utilities screen appears, select

Utilities ▹ Terminal

from the menu bar. A Terminal window will open. In that window, type this:

resetp

Press the tab key. The partial command you typed will automatically be completed to this:

resetpassword

Press return. A Reset Password window will open. You’re not going to reset a password.

Select your startup volume ("Macintosh HD," unless you gave it a different name) if not already selected.

Select your username from the menu labeled Select the user account if not already selected.

Under Reset Home Directory Permissions and ACLs, click the Reset button.

Select

 ▹ Restart

from the menu bar.