An embedded application, developed under the COMDES framework, is built from reusable components implemented as executable function blocks. These are stored in a component repository in a relocatable binary format, whereby the application is configured from prefabricated components, rather than generated. This paper presents a configuration mechanism and a tool supporting the process of configuration, which makes it possible to automatically generate application binaries out of COMDES application specifications. Moreover, the obtained code must not be entirely replaced in case of possible updates, i.e. it is reconfigured such that only a part of the code needs to be modified with a new configuration.