UPD 2 Mr.Claymore I can repeat this bug now. It happens only with "big" config files and happens only when killing the EthMan.exe process in the Task manager. I also see that EthMan is trying to save the config file, even if it is killed abnormally. And I suppose it just has not enough time to finish the save operation and flush the disk cash.
Why do you kill EthMan from TaskMan? EthMan saves data at exit and it can cause this issue. EthMan cannot detect that you kill it abnormally, TaskMan sends normal WM_CLOSE message firstly, in Win7 it waits then, don't know about Win10.