Disabled Tracks in a FCPX Clip

If you will check the X2Pro User Preferences, there is an option to Discard disabled clips.
This option, if selected, makes X2Pro exclude disabled audio clips/tracks from the AAF. The audio from the disabled clips will not be embedded, and the clips will not appear in the sequence timeline

If this option is not enabled, the media will be embedded in the AAF and the clip will still be in the sequence timeline of the AAF,but it will be put at a -96db level.

Give that a try and let us know how that works for you.

Currently when I disable some audio tracks of a video clip and say leave A1 enabled only. When I export XML in Pro Tools all the audio tracks are imported. Is the a way to prevent this?