Removal of "shell" site may cause trouble searching in SXA Scaled environment.
To resolve the issue, download and install the hotfix cpmpatible with the affected product version:
Be aware that the hotfix was built for a specific Sitecore XP version, and must not be installed on other Sitecore XP versions or in combination with other hotfixes. In case any other hotfixes have already been installed on a certain Sitecore XP instance, send a request for a compatibility check to Sitecore Support.
Note that the ZIP file contents need to be extracted to locate installation instructions and related files inside. The hotfixes must be installed on a CM instance and then synced with other instances using standard development practices.