Nope, sv_allowdownload and sv_allowuplaod are only when communicating with the game server directly (e.g. WITHOUT FastDL).
When sv_downloadurl is set properly, and it works, sv_allowdownload and sv_allowupload won't do a single thing.
All the servers I am running and have been running, have been like:
Code:
sv_allowupload 0
sv_allowdownload 0
sv_downloadurl "https://fastdl.example.com"
and it did download just fine from the sv_downloadurl link...
Of coruse, for like CS:S and other games with built-in spray logos, having them at 0 will disable the spray logos, but it won't disable the sv_downloadurl.
Sounds more likely that OP has multiple configuration files, so it loads e.g. file1.cfg with sv_downloadurl "https://A", next it loads file2.cfg with sv_downloadurl "" or sv_downloadurl "https://B", but OP's thread seems a little bit minimalistic, in regards to information that helps to troubleshoot.