Previously fine vessel keeps getting corrupted by a missing part

[Souper]

I'm working on changing a vessel that previously worked in the exact same modpack that I use currently. No new mods were installed since I last flew (or even successfully edited) it, nor were any mods uninstalled. My mods were updated recently though, via CKAN, which might have logs. Despite this, attempts to majorly modify the vehicle consistently result in some form of corruption in which saving the craft at that point (or even undoing my own changes) generates a load failure, which the game lists as "part 4292408338" being missing. I checked Alt-F4 and discovered that it apparently has something to do with the Mk1-3 command pod referencing this apparently nonexistent part.

What could I provide to shed light on this error? What can be done to rectify my vessel file? I have multiple variants of the vessel already saved which load just fine, and in fact, not all modifications result in a corruption. But try anything beyond that and it goes kablooey; in fact, when I got the error by undoing actions, it seemed to generate copies of the craft parts in the exact locations as normal - trying to remove a part after that point resulted in revealing a copy right beneath.

I have no idea how to reproduce this from scratch.

[Souper]

Update: Looking at the vessel craft file, part 4292408338 appears to be a strut connector. My issue also appears to arise whenever that particular area of the craft is modified. Hmmmm...

[Linkageless]

Sounds like a horrendous bug.   Are you able to import this into a separate install with the bare minimum or no mods?  If so, does it still behave the same way?

If all is fine in a non-modded install, does re-adding relevant mods re-trigger this?

Is that strut referenced or referencing another part other than the pod?  (Can't remember which way round it works with struts.)  If the strut is only connected to the pod, it's not beyond all possibility to manually edit it out of the file.  If you're editing an .sfs file, be sure to have keep an identical backup so you can back out those changes.

[Souper]

Update: I have isolated the issue to the Mk1-3 pod. I tried disassembling the craft around it so I could grab a new one, but the editor bugged and didn't recognize when I deleted the pod which was supposed to be the root part. I was able to work around this by starting a new craft file and using the merge feature to rebuild a new identical craft around a fresh Mk1-3 pod, which worked - but the old Mk1-3 that was bugged out refused to be deleted until I saved and loaded the craft. I've been error-free ever since even after tinkering with and removing the struts.