Hi Michael,
We moved your post to the Legacy Yamaha Synths forum because the product has been discontinued for more than a decade now.

I am using Logic Pro X, and the compatibility is fine. However, after working on a song in pattern mode on the Motif, I can only hear the pattern when the Motif is turned on and in pattern mode. Once I turned off the Motif keyboard, the recording in my Logic pro x channel track, do not produce any sound.

This is not at all unusual. The Motif XS is making the sound, (not Logic Pro X, not your computer).

In Logic Pro X you can record two different kinds of Tracks from the Motif XS. MIDI Tracks, or Audio Tracks.

MIDI TRACKs require you play them back in the presence of the MOTIF XS. MIDI is not sound... in all the years of MIDI (1983-present) no one has ever heard MIDI. MIDI is a series of coded messages that represent a music performance. Much like the holes punched in the roll of paper that makes a Player Piano work, the data (the roll of paper) represents a music performance, by itself it makes no sound. You must place it in a suitable Player Piano in order to turn the coded messages back into music (sound).

AUDIO TRACKs are a documentation of the sound, the actual sound of your performing. In Logic Pro an Audio Track will look and behave differently than a MIDI Track.

I have the track channel in logic set to external instrument, using the Scarlett 2i4. The input for the Motif is thru channel 2 of the Scarlett, and the midi is also thru the Scarlett. I can play all the software and record all the instruments just fine. It is just the pattern in motif I am having a issue with, it just won't transfer permanently to logic.

Sorry, I do not know what a “track channel” is nor what an “external instrument” means in Logic Pro. But what you are describing - you want to record Audio Tracks.

Audio of the Motif XS is going to your Scarlet interface... from there you are sending it to the computer.
The Audio Tracks must receive audio from the Scarlet.

Your questions are really about Logic Pro and your Scarlet audio interface... your Motif XS is ready to go...