I read about similar issue in some mod's comments, that particular mod had to do with being able to remove clutter in Sanctuary. Apparently the issue itself is with the cell refreshing. While some mods stumble to it, I guess it can also bug out even without mods. In that particular case, people said it was safe if the armors were moved to some other settlement that was way out of the same cells where Sanctuary resides.
Now, I'm not saying this is the same issue, just sounds similar one. And most probably has to do with the cell refresh one way or another. Are you on PC and if so, do you use any mods?
Edit:
From Scrap Scrap
"Game have issue with CELL update. So when you change a CELL througth esp mod
game will reset stance of all preset CONT (containers) items. That mean
that all Power Armor Frames you scavenge in commonwealth will be reset
to their starting game values (mostly random), but all Frames bought
from merchants will not be affected.
Also every game feature tied to cell will also glitch like hell.
That is not a mod bug. That is a game engine bug.
So if you want to use this mod make sure to preserve your power armor mods."
From Spring Cleaning
"
**The Cell Reset Bug And You**
This particular bug is a very well known side effect of ANY plugin that changes a cells world space. What causes the bug is currently unknown and it's possible it cannot be fixed until the release of the official modding tools.
This bug causes all non-player made furniture and containers to reset themselves as though it was the first time the player had entered the cell. This includes power armor, as frames are considered furniture by the game. Also for whatever reason, cells affected cannot be sprinted in until crossing between it's border and an unaffected cells border.
-Work Arounds-
Store your power armor on only store bought frames, these do not appear to reset.
Store your gear in only player made containers.
Remove any non-player made furniture and containers from settlements to avoid having them reorient themselves and respawn their contents.
Note that using the INI setting does not cause the cell reset, only using the Cell Enabler does."