There is no need to delete any zone information: you can just go to Edit Options -> Station Handling, and set the number of zones to a smaller number, like 8 or 16. Then reboot so the controller starts from fresh. The previous zone information is still preserved, so in the future when you change the number of zones back, the zone name, programs etc. are still there, they are not lost.
The reason to try this experiment is to check whether something is corrupting the Ethernet buffer, which may cause the weird NTP sync problem. One such possibility would be if you have a large number of zones or programs, as soon as you access the controller, transferring that amount of data from the controller to the app / UI may trigger the corruption. So by capping the number of zones, it allows us to tell if this might be the root cause of the problem.
Firmware 2.1.9 uses a different library and mechanism to handle Ethernet connections, so it’s possible this is a new bug that wasn’t in previous firmwares.