I work with an external USB 3 Wifi adapter as well. Here are some challenges I observed which might be helpful:
- If you work in a home Wifi with several repeaters check if you did the setup at a different location than the actual observation site. I did and it turned out that the WiFi adapter connects to a hardware but not to the Wifi network in general i.e. it tries to connect to a certain box even a repeater in the network with the same SSID nearby provides a much better signal. Indicator: when testing indoors things seem to work much more stable
-Check if besid the WiFi dongle the Raspberry is still connected to your home WFi directly, If so, supress this connection in the network settings (main menu)
- Check the VNC settings (icon aat the top right of the Pi desktop) and uncheck that it disconnects when the connected device is inactive. I don't have a Pi around to check the exact wording at the moment
Maybe one of these things could help you to get closer to the root cause.