It depends on the workflow of the given render farm. I understand that you are using a farm which just renders your project using automated workflow.
In general, if the render farm offers a plugin for uploading your project, it should relink the proxy and upload it to the farm with the whole project. The proxy, like other assets such as textures and caches, should be properly linked in the scene or use relative paths if your setup allows it.
If it doesn't work, then I'm sure it can be relinked on the farm's side, you would just need to contact the support team and upload the file. The question is if that particular farm is ready for such semi-manual workflow and how long it takes to get a response.