This is normal.

When you start with a Performance before adding anything to it - all of this Performance's Super Knob connections (and, by the way, system effect settings) are defined. It's possible that the Performance you start with before adding anything has Super Knob tied to ALL of the available common assignable knobs and all of these knobs may be tied to Part level knobs downstream already.

When you Add or Merge in a Part to the existing Performance - MODX doesn't "know" what to do. There will likely be conflicts with existing programming from the initial Performance. MODX does not attempt to guess how you want to connect the merged/added Parts to Super Knob (and also the new Part likely loses its previous system effects and master effects). Therefore, at this juncture - it's your responsibility to make tradeoffs (if necessary). Decide how to "rewire" the added Part under Super Knob control. You may need to delete existing Super Knob assignments. Or you may need to connect up the new Part's Part level assignable knobs to different common assignable knobs than the original Performance this Part comes from. These are all choices Yamaha elected NOT to automate and leave up to the programmer to decide.

Even if your starting Performance has no Super Knob assignments that would conflict - the policy remains. If this is true that your starting Performance needs no Super Knob control and your merged/added Part(s) do - then I would suggest flipping your "build order". I'd start with the Performance you currently merge in as the second step and make this the first Part you start with instead. Therefore, this Part (or Parts) will have all of the Super Knob connections in tact and now merge/add in the Part(s) you initially had under the lower Part numbers. The decision of which one to start with can be determined by how much work it would take to reconnect what you would need to reconnect. Partly by the system effects and which Part's sound (after merge/add) is incompatible with the other's system effects. Although this you can also manually change. And also, to a lesser degree, the order of Parts with respect to priority in the events of polyphony limits (note: you may not ever have a polyphony issue - this would generally be a secondary or tertiary consideration).

Jason, thank you for such a detailed answer - everything became very clear! Indeed, there is a certain logic to this.

Please see this thread for how the MODX/MONTAGE handle your Common/Audio (Super Knob level of the architecture) assignments - they are not lost. They are maintained but you must review them - decide if you want to use them - each-by-each. But no heavy reprogramming is necessary. You simply update the assignment telling the MODX *where* your newly merged Part is now located. As your review them the Control Assignment is activated in tact - except now it will directed to the appropriate PART #.

Here is how you can reactivate those you wish to implement in this new Performance. They are not automatically implemented for the reasons outlined in this post:

Link -- How Super Knob assignments are handled when "Merging" Performances

If when you review the anchor (Part 1) Super Knob assignments, all 8 Common Assign Knobs are used, you can piggy-back your 'merged' Part's assignments to one of the existing Common Assign Knobs... yes, you can stack multiple items on any Assignable Knob. The attached example is for the MONTAGE - if you need a copy for the MODX we can post. Let us know.

Bad Mister, thank you so much for your answer! With the help of your detailed instructions, I will study the super knob architecture.