You are not supposed to run encore prod on your production machine (in the same way you are not supposed to run composer install in that machine).
Building & Deploying are different steps.
You'll need to run all the build steps in a different place (at the very least a different directory from the one you are using to actually serve the application), and then deploy the generated "artefact" (e.g. the result of your build process).
How you do this depends on your serving infrastructure and deployment process, but it can be something like:
- copying the files (
mv,cp, etc). - transferring the files from your build machine to your application server (
rsync,scp,ftp, etc) - build a Docker application image and push to a container registry.
- etc.
Whatever you do, you need to avoid running a long process that modifies files that are being actively served.
Build processes can be long and it's fine that they are long (as much as we'd prefer they'd be sorter), but deployment processes should as short as possible.