Do you have your wifi setting in their own profile or mixed in with other settings?
All MDM's removed profiles created within configurator upon connection, I never bother with configurator because it just creates problems, my suggestion is buy an Apple lightning to USB camera connecter and a Apple USB ethernet adaptor and make yourself a ethernet adaptor to setup iPads, I find this way more efficient than plugging devices into a computer and mucking around with configurator and it will solve the problem you have.
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