I experienced this problem yesterday, had to call ESRI today. We found a work around but the main issue; if I create a brand new map in AGOL, the option to take the layers offline is absent and we could not figure out why. All the layers in the map had sync enabled and were editable etc. But of course the download option in Collector was not available.
Eventually I took a map which worked previously, and added the same layers to it, renamed it, and it worked fine. The download option came up in Collector etc.
The Rep is hoping it is a one time, one off situation. But if I cannot create a new map and see the option to download, and have to use only previous map, I am a little dubious that others won't have the same problem. But hopefully the work around helps.
Cheers