You may run into an issue where your built assets are not appearing on your server.
When you run a deployment with a build pipeline configured, DeployHQ will only upload files that have changed since your last build. If for any reason you have removed built assets from your server, you'll need to force them to be uploaded again.
This can be done simply by running a new deployment without the build pipeline enabled, then another one afterwards with the pipeline enabled once more.
This option can be accessed via the Advanced area in the new deployment screen:
Then once a deployment has been run with the build pipeline disabled, simply repeat the steps to run another deployment with the build enabled.