It sounds like you've accidentally changed the output for those two tracks. If the output is set to anything other than L&R or L&R(dr) then the corresponding audio from the tone generator bypasses the send effects (explaining the missing knobs) and depending on your audio routing and monitoring they may become totally inaudible to you.

This setting can be found in the bottom right on the edit screen under Part Common: General in the VST (screenshots attached).

Sounds like your using one of the Templates that assigns the A/D Input to FW13 & FW14 as the default.

From the following article: Motif XF Setup Templates for Cubase

Templates:
Sets up the Motif XF VST for a number of PARTS as follows:
PART 1 goes to the L/R
PART 2 goes to FW1/2
PART 3 goes to FW3/4
PART 4 goes to FW5/6
PART 5 goes to FW7/8
PART 6 goes to FW9/10
PART 7 goes to FW11/12
AD PART goes to FW13/14

PARTS 8, 9, 10, 11, 12, 13, 14, 15, and 16 are routed to L/R

The problem with using Templates is they don’t always do exactly what you want to do... I’m sure this is it because it’s the AD Input to 13&14.

Yes!
I changed output select for those tracks in the VST editor, and the sound came back.

I wasn't aware of using a template. If I did, It was by accident. I'll investigate further to figure out how that happened.
I can't thank you guys enough.

Extra Credit:
The default Mix Template when you open the Editor VST in Cubase sets the OUTPUT SELECT as outlined in my previous post. The following articles will show you how to create your own MIX TEMPLATES (which you can store in ROM on your XF. The 3rd link is a video that shows how to set what the XF setup defaults to when you open the Motif XF VST.

Additional Reading: Explains how to create and store as many as 32 different Mix Templates onboard the XF:
1_ Mix Templates
2_ Cubase Templates for Motif XF/ MOXF

Additional info: I shot this six years ago... it shows how to import your favorite ‘starting point’ Mix Template to Cubase as the Default Preset...

https://youtu.be/QYtIMykyPo0

Final Word —Working Smart
The referenced articles show how to create your own Mix Templates. 32 of these can be stored onboard the XF itself.
The referenced video show how you can transfer one of the Mix Templates to Cubase.

When you develop a workflow... and please realize you will not know exactly what works best until you’ve completed a number of projects. I recall writing those articles and shooting that video because in my talks with many, many end users I found those who were having issues with computer setups, were tripped up by some basic misconceptions. Many thought that *setup* was way too complicated and most thought they would need to do this setup EACH TIME they booted up.

Of course, only half of that fear is founded. Yes, setup can be complicated, but No, you do not have to do it EACH TIME you want to use it. You need to set it up properly once, then use the computer’s best and most endearing feature: the ability to ‘learn’ your setup and instantly recall all of your preferences for setup.

When you create an XF “DEFAULT MIX” of your own, you can then ‘teach’ Cubase to open and restore that MIX (in every detail) to your hardware (XF). Not only will Cubase setup itself for the type of recording you want to do... it will automatically open the Motif XF VST Routing scheme, restore the exact starting point settings that you use most often to your synth.

I say it often, if you find a factory Template that works for you, it is serendipity. They are very general. The factory default sets the A/D Input to FW13&14. As I state, I set my defaults so all internal Parts are routed to the MainL&R, (I make individual Out assignments, only as necessary)... I also prefer the HD Hall over the factory default of the Rev-X Hall, etc., etc., and since my A/D Input, if used, will be a Mono In and I don’t always use that input, I set it to MainL&R and will change it only as necessary. Remember these are your personal preferences!

Mostly you want to develop your own workflow, based on what *you* do most often, then construct your own Templates! When you open *your* Template it is as comfortable as you own slippers — they fit perfectly!