I finally managed to reproduce the disappearing socket bug on PC, patch 1.12 and I have 2 save files where you can observe the disappearing socket. Its on Oda. The first save is after Oda has been defeated and the player is right in front of his body with the items unlooted. This save file also demonstrates the bug where loot is reset to level 1 upon save/load, so both items of clothing on Oda's corpse have level 1 stats and one of them was downgraded to epic permanently because thats the minimum quality level apparently.
The other save file is just before the Oda fight. My V is level 43 and is OP as balls so you can kill him in 3 katana heavy attacks. You can dance around the arena and kill him at different xyz coordinates to randomize his loot if you want to test it on different items (and I confirm it is reproducible on all procedurally generated item he drops).
He always spawns Jinchu Maru and 2x items of legendary clothing - 1 of them is always Arasaka Polycarbonate-Laced Bulletproof Aramid Vest and the other 1x is procedurally generated from baseDropBag (this contains mostly Arasaka themed clothing and rather annoyingly, an Arasaka Hasmat Suit which is just a special skin).
If the item has 1 empty socket and you pick it up, the empty socket will always disappear. This happens if the item has 3 sockets (2 mods, 1 empty, 1 me-thrill), 2 sockets (1 mod, 1 empty, 2 me-thrills) and 1 socket (0 mods, 1 empty, 3 me-thrills). It only happens if there is 1 empty socket.
It does NOT happen if the item has 4 sockets (3 mods, 1 empty, 0 me-thrills). This is probably why I've never seen it, because I persistently save scum for max sockets. I am pretty certain this bug is related to me-thrill as the only scenario where it does not manifest is if the item does not have a me-thrill mod in it.
In the case of the 1 socket roll, the only socket disappears upon picking it up so there are no sockets to interact with to put in a mod, to get the socket back. In all cases, the socket becomes interactable again if you replace an existing mod with one in your inventory. This has already been shown in the thread but to add to that, the reproduction rate is 100%.