Across all my captains, old and new, switching a ship will scramble the bridge officer skills in the loadout. Captain abilities, console abilities, etc. are all where they're supposed to be; it's just the bridge officer abilities (and sometimes reroute shield power abilities) that are affected. This also marks the loadout as having "unsaved changes". I cannot discern a pattern to the scrambling: some skills are removed completely while most are in different positions, looking like they swapped locations with other skills that are also scrambled.
I have gone to great lengths to keep my loadouts safe. I save them multiple times in TFOs or patrols or other non-social areas to avoid any kind of other-player or other-mode code interaction. I only switch ships at a base with a ship selector officer. (Switching from sector space on on a space map would always corrupt the layouts before this, so I just stopped doing it althogether.)
I have noticed that I can load the layout without errors from the ship selection screen. For instance, I can load the layout before switching to a new ship, and when I switch to a new ship the layout remains unchanged. Just switching to a ship without pre-loading the layout however does result in "unsaved changes".
If I have a ship that I've successfully pre-loaded the layout from the ship selection screen, the "unsaved changes" message appears and the tray gets scrambled upon transitioning to a space map. I have not found a way to transition to another map (earth orbit, TFO, patrol) that does not re-validate the ship and break the loadout.
Besides scrambling bridge officer skills, one other thing often happens: the reroute shield powers move to the "first, lowest, open slots". When I first equip a ship, I moved those five skills to skill bar 7, then hide that skill bar. This problem has been around for years, so I am not sure if it's related or not.
I've tried to eliminate the other potential issues: I finish all duty officer missions so duty officers in the load-out are not on assignment. I do this with captains that have not recently leveled a reputation to Tier 6 which "unequips" the old versions of starship traits for new Level 2 ones (this is really, really annoying). I can't think of a way starship traits might be bugging it out. Most don't have console-granted skills like bio-molecular turret three-piece.
One thing I haven't been able to test well is if bridge officer specializations after the loadout was saved might be breaking something, especially if the same bridge officer has two specializations and uses both in different layouts. I've mostly controlled for this by verifying the officer has the same specialization active as is used in the current layout (and that layout still breaks), but I have been using specializations much more as my fleet contains more C-store and legendary ships.
This problem has gotten so consistently bad that I'll either switch captains or just ignore things like endeavors rather than switch a ship on the same captain.
0