Quote:I am not using the "Zenphoto Tool" for a backup
The tool is only to backup your database.
Check all your zpMasonry files to be absolutely sure ther is no malicious code inserted somewhere.
If all is clean you can of course use those files again.
Quote:Why is it better to make a custom copy than changing the original theme directly?
That refers to official themes. When you want to modify one of those themes it's best to make copy of it, rename it and then make the changes.
This way your theme will not be overwritten during an update.