Yes. It's not a big deal. All posting journals and check registers get purged at year-end anyway (I like the word purge instead of clear because clear has another meaning in Payables).
The fact that you could even accidentally purge your check register means you are not using the latest version of Payables. In the latest version it's not even an option. So you might want to install the latest upgrade.
If you absolutely need to see the check run, you can look at the Check Number Audit List (under Payments), and you will see most of what you need (and a whole lot of what you don't need).
Steve