There is a other thread here where somebody actually suggests that there is a method of removing an Asobo airport if it clashes with a 3rd party one.
Scroll down a bit. There is a post regards using the scenery editor to delete an airport.
I wasn’t aware of this possibility and have not tried this method, however I have had 3rd party airports disrupted by Asobo world updates in the past and in those cases it’s simply a matter of waiting for the 3rd party Devs to update their product.
(In my case it was Orbx and Flytampa both of whom released their updates really quickly and as I had bought these from external vendors rather than the marketplace I had access to the updates as soon as they went live.)