I noticed that dropping a data file to the server, and referencing it as "knime://server/folder/data.csv" in a file reader works fine in local workflow - but copying the workflow to the server then executing via the web portal results in a file not found error.
Are you using the default mountpoint ID on your server? If not, you will need to either edit this or try another approach. You could also, for example, use a workflow relative file pathe which would let you store your data and workflows in a workflow gropu and then reference them using knime://knime.workflow/../ /data.csv