Are you sure your equipment didn't just get moved around? The game tries to optimize your equipment for power or something (which is incredibly annoying as it keeps removing my Tank equipment off my GNW Neji :L).

maybe it was just swapped from your other items.

Can confirm I lost magatams on a old char :/

So to avoid this, i'm swapping them by archetype: I swap the tanky ninja with another, healer with healer, etc...

And if I need to change the whole team, I manually remove magatamas then pput them back on.

i can confirm this too but no screenshot either ( i though it need a video atleast ), and lost magatama when swapping ninja from left to right or just complete remove all ninja and ur main are the only one left on the left side ..

- this occurred only sometimes ( missing magatama )
- sometimes only occured when some ninja in your team had empty magatama, so its just go rolling to 1 ninja or just completely missing
- sometimes its not just magatama, its your gear lvl, if some stats of ur gear of ur ninja are not full strengthened, ex : lvl 18 life but lvl 1 attack etc, its getting rolling again and sometimes im seeing some stat of the gear just resetting to lvl 1 ...
- and all occurred while u swapping ur ninja on ur team ..

kinda weird but im getting this horrible act "sometimes"

You can't lose your magatamas.

Okay Small Update:
I finally understand what exactly goes on.
On the Ninja Pannel If you place one Ninja on top of the other one it will Transfer the Magatamas To the other Ninja. Lets say I have a Neji In the Active Squad if I throw a Hinata on top of him All Neji's Magatamas will transfer to Hinata.