no, it shouldn't be a problem.
you don't really need to run the WA uninstall routine when installing the update 6.0.6.
simple open the Extension manager, uninstall the 6.0.5 version, install the 6.0.6 version, then open DW and a php page to start the installation process for 6.0.6.
it will overwrite the files from 6.0.5 when running the WebAssist installer.