I Have a RPi 4 with a Conbee II stick running the Deconz integration. Recently I connected my home network to another home network through a VPN in a site-to-site configuration. I did this because I wanted to use one HA installation at two locations.
At the second location I connected a hacked Lidl zigbee gateway through ZHA and that went fine, but the ZHA gave back some ghost devices it had “found”. I can’t seem to delete the devices and it also merged the devices with the Deconz devices which gives some devices two entities.
In the past I switched ZHA for the Deconz integration on the Conbee II stick. I deleted the ZHA integration because I wasn’t using it anymore.
I don’t know how to solve your issue, but I can tell you that I run both ZHA and Deconz on two different ZigBee USB radios at the same time without problems*. The devices that I have moved from one to the other are listed as both ZHA and Deconz, but that’s only because the HA database recognized the device when I re-added it to the second one (from Deconz to ZHA or vice versa) and added the integration name to the entry instead of replacing the old one. So I don’t think having it show up with both integrations is your problem.
*I do this because many of the bulbs are on z-wave in-wall switches so turning the switch off cuts their power and makes them leave the network. Now I have the non-bulbs on a separate network so they don’t lose connectivity.