Not sure what steps you followed but are you able to work with new documents (add, move and delete) in the installation you are having problems with? If not, your documents directory location and/or permissions are incorrect.
If problem is limited to old documents and directory location+permissions are correct, then you probably changed the root for emr software during the upgrade. Make sure directory
/home/mysite/public_html/emr/sites/default/documents/ exists with all documents if your emr scripts are in
/home/mysite/public_html/emr/directory as they were prior to the upgrade. Developer elected to store absolute path for each document in the database. That means if old directory structure is not replicated, you get error(s).
If you changed directory structure during upgrade, you will have to fix the entries in documents table.