We also recommend creating a backup of the previous version to have an ability to revert it in case of problems with the new one. If you configured user restrictions, save the access-config.json file. You need to save the whole conf subdirectory which is located in FLS installation directory. In short, you need to save configuration files with previous settings, replace old FLS's program files with the new build and then place configuration files back.
In-place upgrading is available from build #12431 and is similar to the new installation procedure. After registration, new FLS will take license information from JetBrains Account. In this case, you need to repeat the whole procedure of configuring this new instance of FLS and link it to your company profile. If you have very old FLS version (before build #12431), we recommend installing one of the newest versions.