I've lately been noticing that a part of my inventory just disappeared every so often and I found the issue. It seems to be some weird error with mech armor toolbelt equipment, like it turns off whenever you ride, removing those slots from your inventory and then after finishing you get them back but without the items (bots seem to be added to the nearest network, other items simply get removed).
It is a very peculiar bug as sometimes it doesn't even remove the slots themselves but their filters.
I am uncertain as of now why this happens, but it certainly has to do with some automated disabling of the toolbelt.
(It might be some way that you have worked around the power armor having it's modules disabled resulting in this gllitchy toolbelt equipment reaction)