You can remove the system using Account section from the Pulseway WebApp. Then from the left menu select the systems tab -> Configuration -> select the required Organization-Site-Group.
And then please remove your system and save the changes:
Note: that the system, which are you deleting should be online at the time when are you deleting it, because if the system is offline at that time, then the reconfigure command will not be sent to that system and that system will re-register with our account as soon as it will come back online. However if the system no longer exist, then simply delete it.