Sorry, probably didn't explain myself too well there. I created a configuration file (conf 1) when I built the original package. When you set CreateDeploymentUtility to True it adds that configuration file to the deployment manifest. On the production server then, when I run the manifest it displays the configuration file I added to the package (conf 1) and allows me to change some of the variables in there before deploying to the prod server location. I didn't change any values there, and so it deploys this configuration file (conf 2). When I then create the sql agent job with a step to run the ssis package (file store), I must have added in conf 2. I let that run for a few weeks until I was happy it was stable. I now want to swap it to another configuration file. I copied conf 2 to another file, conf 3, then edited conf 3 making the necessary changes. Now we're going live I thought it would be just a job of removing conf 2 from the sql agent job and adding in conf 3.
I've eliminated the possibility of it being a read access issue. The agent job was running as my sql server agent account. I added in full file and folder permissions to the config files and folders. Re-ran it and still the same issue.
Stuck again! Could it be a caching issue with the config file? Do I need to restart the sql agent service may be?