Obviously if Workshop content is taken down from Workshop, you'll not be able to receive it anymore. You'll keep it in theory on the server but people will not be able to receive it, unless you have a backup route (old redirection method) in place to distribute the file then.. if that is what you mean.
This is how the engine work for the INI, you need the INI file to let the engine know the map exists and let the webadmin allow you to use it, it is still annoying to have to write a text file manually but if you're really in need to NOT write it yourself you can still create a simple script like bash file to automatically search for specific file type (like ROE) in specific folder (like CACHE) and then look if a corresponding file (the INI file) exists in the CONFIG folder, and if not, automatically create the INI file regarding the specific map prefix (VNTE, VNSU, or VNSK). I did that for the people I host RS2 servers for (actually they don't use Workshop and still upload the map files and use redirection and the script creates INI file if needed and duplicate the map file to the webserver for the redirection, but it would work exactly the same for files from Workshop system), but as I host on Linux the script will not be compatible with Windows, but pretty sure you can achieve the same on Windows.
Maybe one day they'll make it possible to have the config files for Workshop maps delivered with Workshop too, but do not have too much hope because I eared about that since so long time that this does not seems a priority at all..
edit: when I think about it AMG/TWI could make exactly what I'm talking about and have an optional .BAT file delivered with server files that server admin could use to create INI file automatically if server admin eexecute it in order to automatically create the INI file for them.