While editing an Excel file fetched from intranet and not from local computer if you what to make a change into this file and save it, it will be saved on the temporary local folder (I think) and not on the initial intranet location. Therefore, if you are uploading a new version, if will bring the version from intranet, which does not have the change made.
It would be nice if Companion will understand that the source of the Excel file is on intranet and will pass over this information so that Excel will understand also that the file is on intranet and when saving the file from within Excel, this will be saved into the right place (intranet).