Is it okay to delete certain System files if you have a backup copy available?

It's hard to answer without specific knowledge of what was done. However if EVERY System file has been replaced with an exact copy and renamed back to what it was, I expect all will be fine.

If I were in your shoes, I'd restore the last Time Machine backup from before the tampering. Even if all seems fine now, maybe you'll find that, say Software Updates don't work correctly in the future because of something he deleted. It's hard to tell, your description of what happened is vague.

If you don't have such a backup, then I guess you don't have a choice. I think the real test will be when you shut down and then restart your computer. I suggest making a good backup of all files (or all your key files) before doing that in case you have to reinstall the operating system and then restore your files to a the new system.

If you lost some files in Preferences it isn't too serious. Whatever is missing would be recreated (with default preferences) by those processes that require them.

Updates, if it is the same one I am looking at with a ProductMetadata.plist and a folder named zzzzddd-dddd (d's are digits), is related to software update. The plist is updated each time you run software update. So try doing a Software Update and see if there's a problem. If not you're probably ok.

Maybe the thing you need to do is set up the computer to require a password once it's been inactive for more than one or two minutes so this can't happen next time ...

If they are exact copies they're data, no one is going to know the difference.

It's difficult to remove critical system files just by dragging stuff to the trash. Data can be deleted pretty easily, but important system files typically can't be deleted unless you use Terminal and the sudo command.

Kids, aye? You gotta love 'em... 😁

The answer to your first question is NO. Your system is currently working and the last thing you want to do is start messing about trying to delete and copy system files. What you do is, first:

1. Restart your computer in 'Safe' mode. This will sort out any critical system issues. To do so, see the article here:

http://support.apple.com/kb/HT1455

2. After Safe mode has finished, logout and log back in normally.

3. Run Software Update

4. If you encounter any errors in the previous three steps, make an exact note of the error message and when it occurred, then post back here. We will help you sort the errors out. Likewise, if everything appears OK, but you encounter some problem later on in use, make a detailed note of the msg and the circumstances and post back.

Once you've done all that, the second thing you should do is set your machine to require a password after some minutes of inactivity. To do that, go to

 > System Preferences > Security > General

and check 'Require Password 'IMMEDIATELY' screen saver begins. Then choose 'Show All' in the task bar of that window, and choose 'Desktop & Screensaver' and set it to something like 5 minutes (all this assume you have and know your own logon password, of course!)

The third thing you do is buy a cheap, USB external disk and start using Time Machine so that you have a backup.

Good luck!