Into the dll.xml and exe.xml folder in the C:\Users\Username\Appdata\Roaming\Lockheed Martin\Prepar3d v3 folder
An .exe should be added ONLY to the exe.xml file. If you added it to the dll.xml file too, it will probably ignored, but I suggest to remove it anyway.
If you are using P3D 3.3 and less, the installer should have added the correct lines in the exe.xml itself.
If you are using P3D 3.4, the line in the exe.xml is not needed anymore, because the executable will be loaded from the add-on.xml file instead, which is the more "native" P3D installation method.
However, P3DV4 had a bug in the initial release (which has been fixed now) that, if you have your EXE.XML corrupted by another application defective installer, or if you have edited it by hand, it will prevent all the other executables from loading, even those not using it. I guess P3D V3 might have had the same bug so, it's possible that, if you had a problem in the exe.xml, it prevented to load Couatl.exe from the add-on.xml, just like in P3D V4 without the Hotfix.