Unable to change App icons: Sierra

Do a backup, using either Time Machine or a cloning program, to ensure files/data can be recovered. Two backups are better than one.

Try setting up another admin user account to see if the same problem continues. If Back-to-My Mac is selected in System Preferences, the Guest account will not work. The intent is to see if it is specific to one account or a system wide problem. This account can be deleted later.

Isolating an issue by using another user account

If the problem is still there, try booting into the Safe Mode using your normal account. Disconnect all peripherals except those needed for the test. Shut down the computer and then power it back up after waiting 10 seconds. Immediately after hearing the startup chime, hold down the shift key and continue to hold it until the gray Apple icon and a progress bar appear. The boot up is significantly slower than normal. This will reset some caches, forces a directory check, and disables all startup and login items, among other things. When you reboot normally, the initial reboot may be slower than normal. If the system operates normally, there may be 3rd party applications which are causing a problem. Try deleting/disabling the third party applications after a restart by using the application un-installer or by using the developer’s uninstall instructions. For each disable/delete, you will need to restart if you don't do them all at once.

Safe Mode - About El Capitan
also Sierra

Safe Mode Startup – El Capitan. also Sierra

If it works in the Safe Mode, try running this program when booted normally and then copy and paste the output in a reply. The program was created by Etresoft, a frequent contributor. Please use copy and paste as screen shots can be hard to read. On the screen with Options, please open Options and check the bottom 2 boxes before running. Click “Share Report” button in the toolbar, select “Copy to Clipboard” and then paste into a reply. This will show what is running on your computer. No personal information is shown.

Etrecheck – System Information

You enable SiP again. No need to disable it.

You do getinfo on the app you want to change,

then find an app or folder or file with the icon you want and do getinfo on that, put the getinfos next to each other for convenience.

Now click on the icon you want (in the getinfo window), select "copy" in the finder Edit menu,

Now click on the icon you want replaced (in the other getinfo window), select "paste" in the finder Edit menu.

That does it.

I've got a MacBook Pro recently and like to customise it, which means changing App icons.

You may not do that with signed apps. You may only do that with unsigned apps or those using an obsolete signature.

That is a different question, but the answer remains the same. You asked about changing app icons. The Applications folder you are asking about now is not an app. It is a folder owned by root. You may not change its icon.

The fact you are able to do that with the Mini indicates its Permissions are messed up, which can be difficult to rectify. Attempting to modify the Mac's UI in the manner you describe has always been a popular way of corrupting macOS. I suggest you don't try fixing what isn't broken.

I agree with John. If you do it, the icon will change but not show the icon you wanted to use but a default "non-icon" indication

It works perfectly well.

There is something else on your mac.

Download and run etrecheck.app and post the list here.

etrecheck.com