this is trivial thing as soon you gold or red those equipment it doesnt matter anymore whoever has it
the only thing maybe the Magatama side

for the sake answering your question
I do this all the time
Main always on Top so nothing will change
the other 3 will change if mismanage your positioning

assign your Tank, DPS, Support
when you switch ninja unit assign to their respective role
ex. Hinata Tank to Gaara Tank and not Hinata to Sasuke because Sasuke will get the Tank equipment
and so on

Main character equipment will not change because you cant remove the main in the formation

Go to character, double click on the equipment you want to change. By doing so it will be in your inventory.

Again do the same thing on the ninja you want to give that gear.

To avoid this situation, don't remove a ninja from your lineup. Simply place the new ninja you want to include in team, on any of the ninja you want to change.

Oh, thank you a lot, you are my savior!)