Try this. Go to Settings > Apps > Health > Data Access & Devices. Under Devices, select the devices you are actively sharing health data with, tap and select "Delete All Data from *devicename"
After that, go to Settings > Apple Account > iCloud > Storage > Health > Delete Data from iCloud. Wait until the process is finished and you will be sent back to the iCloud menu.
It is a good idea to be connected to WiFi when doing this, as iCloud updates a little randomly if you are using Mobile Data, depending on what settings you have set up.
Finally. Try turning the iPhone off completely, and then turning it back on. Go in and check if your data has disappeared from iCloud. It is a good idea to restart your iPhone once in a while, as this will start a little cleanup.