This happens (or seems to happen- because, there is nothing wrong) when you are unaware of how Pattern mode works when archives your recordings to Pattern mode. Each recording in Pattern mode is given a Phrase number 001~256. If you are unaware of how this works the symptoms you describe can happen.

Also using the wrong COPY JOB to accomplish a goal can cause you issues. Once you start recording please realize that each new recording is given a number (and can actually be named). This number tells you which Phrase you are working with...

Record four Tracks in a blank Pattern in Section A
Press [F4] PATCH
Here you will see the Phrases identified as 001, 002, 003 and 004

Let's just say that 001 is your Drum Pattern.
That Phrase, 001, can be activated in any Section [A]-[P]
Go to Section B
On the [F4] PATCH screen, "patch" phrase 001 to Track 1 of Section B

If you edit, change or delete the data in Phrase 001 you do it to Phrase 001 everywhere it appears.
Add a crash to Phrase 001, it will edit everywhere Phrase 001 is "patched"
Delete the data in Phrase 001 in Section B, it alters every other Section that contains a Phrase 001
"My Moxf 6 sometimes deletes other tracks in pattern mode"

Yep that is exactly how that happens.
If you don't know which Copy Job to use, you can wind up Copying the Phrase to a new Section, instead of Copying the data in the Phrase to a new unique Phrase number.
Copy Event
Copy Phrase
Copy Track
Copy Pattern

If for example, you want to use the same drum groove in Section B that you used in Section A but would like to edit it so that it is different (say in B it starts with a Crash and adds percussion) you must COPY 001 to new "unique" Phrase Number.

Using "COPY TRACK" would be the correct way... it would copy the data in Phrase 001 to the lowest numbered empty Phrase... 005.
Phrase 005 will sound exactly like 001, but you can now add your crash and percussion *just* to Phrase 5.

Until you appreciate how the Pattern mode organizes your Phrases, you will continue to have issues.

Required reading: COPY JOBS

Thank you so much for your detailed answer.
I will work today on this and go through this step by step.
I am new to the Yamaha workflow. I used to have an Roland xp50. I think Moxf is a very good station with wonderful sounds. I added an Roland xv5050 to it to get some of the great Roland sounds too.
Love that setup.

Again thanks for the help in solving this problem.
Noren