Hopefully, the timeout error was a fringe event. Let me know if you see it again.
In custom themes, you choose to override one or more files from the original theme with your own versions. Or you might choose to complement it with new files. When the underlying, original, theme gets updated, the untouched files (files that your custom theme does not override) gets updated automatically.
Files that you have made changes to will need to be manually updated to merge in the updates from the original theme. If you want or need them.