I don't know what you did to "removing GSX Pro completely" but, if you did it in the only correct way, by using the "Uninstall" button in the FSDT Uninstaller, the uninstaller would have removed the Couatl64_msfs.exe entry from the EXE.XML automatically.
In fact, the entry is removed even after you just UNLINK GSX Pro, which is what you are normally supposed to do if you just want to Disable GSX temporarily, without going through the hassle of reinstalling it again should you need it. GSX won't have ANY ( repeat: ANY ) effect on the simulator with it's Unlinked since, Unlinking both removes the links from the Community folder AND removes the Couatl entry from the EXE.XML, Relink is the opposite.
If, instead, you tried to remove it manually for some reason, you need to clear up the EXE.XML entry manually.