UPDATE 19/9/18: It has been fixed in 126.96.36.199 version of Plugin Registration Tool https://www.nuget.org/packages/Microsoft.CrmSdk.XrmTooling.PluginRegistrationTool/188.8.131.52
If you use 9.0 version of Plugin Registration Tool to update your assemblies in Dynamics 365 you may encounter the following exception:
ERROR: Occurred while checking whether the assembly exists
The PluginType(00000000-0000-0000-0000-000000000000) component cannot be deleted because it is referenced by 1 other components. For a list of referenced components, use the RetrieveDependenciesForDeleteRequest.