There is a lot of misunderstanding about #6585 (see this thread). It seems unlikely that it alone would be the cause of your problem unless, for example, your ethernet cable has been unplugged for the past couple of months. You probably would’ve noticed that in other ways!
Since the qubesctl commands are just the command-line equivalents of the graphical Qubes Update Tool, if the former worked for you, then that doesn’t really explain why the latter seemingly didn’t. In this case, it would be useful to know what happened (i.e., the actual output) when you tried running various update commands in a terminal.