Are you sure you don't get a slight difference in the URL (even going from http to https could cause that kind of issues ? btw there is a flag in registry to indicate https ('HTTPS' dword value in HKEY_LOCAL_MACHINE\SOFTWARE\DSoft\Efficy\Web) , so even after passing a reverse proxy, the <%GetFileUrl()%> or <%GetAppBase()%> should reflect the https flag).
I don't understand why you use GetAppBase, because your are talking about file download. In standard the filehelper module is designed to process urls from the data-file-url attribute of a file, which uses GetFileUrl.
Which version are you in ?