If you plan to update the operating system on a Linux endpoint to a major release, the agent on that endpoint should be put into disabled mode before the OS update. This would be true, for example, for upgrading from RHEL 6.8 to 7.3.
For minor Linux OS updates, as long as both the current and upgrade version are supported by the Carbon Black App Control agent running on the system, you may leave the agent in its current Enforcement Level. This would be true, for example, for upgrading from RHEL 6.7 to 6.8.
Also keep in mind that your current agent might not be supported on some versions of Linux. Before updating the OS, see the release notes and also Supported Carbon Black sensors and agents on the Release Information and Downloadssite to check current OS support information for your agent version.