I edited the palette I was using for the majority of the game, added a new palette to a few other rooms, and then played it to take a look.
Noticed immediately that maybe around half of the Items in the game had disappeared from their Rooms.
This includes Items that were using a fourth colour (manually added to the game data). Sprites, tiles, etc were unaffected. The few Items that weren't affected (all instances of one Item in the whole game seemed to be either affected or not) didn't appear to be special. Some had Dialog, some didn't. Each palette's Item colour was easy to differentiate between the Background and Tile colours. Using the Avatar to interact with where the Items had been before didn't seem to do anything, so they weren't just invisible. Their graphical data was still the same (including extra colours) in the Drawing tab and thankfully their Dialogs were still there too.
This also happened to items in Rooms that were not using the edited palette. I hadn't edited this main palette since I started making the game.
A while before editing the main palette, I'd added one more palette for one Room, which didn't seem to result in any issues.
I haven't done anything with the Inventory tab yet.
I haven't tried to repeat this to see what happens, but will report back here if it happens again.
I hope some of this info is useful! I also have the palette data if that helps.