Which keys in particular are you struggling to find? I mostly just tested with the Machinery and Unknown keys while developing this mod, so I might have overlooked high-value ones that are harder to get. There is a minimum time before each item on the map is allowed to despawn, but it's linked to its proximity to a possible spawn point. If you spawn relatively near it and right run to it, it's unlikely the mod has been allowed to despawn it (at least in theory). If you spawn far away, you may be SOL (like in live Tarkov).

You can manipulate the loot ranking for keys by adding an entry for "543be5e94bdc2df1348b4568" in destroy_loot_during_raid.loot_ranking.weighting.parents like this (shown below the existing last entry):

I would start with -20 for the weighting, but you'll likely need to tweak it for your liking (the more negative the value, the less likely it will be despawned). I'll do my own testing with the keys you're struggling to find too, but I probably won't have time until next weekend.

After you restart the server and launch the game, the loot-ranking data will be updated. After this happens, you can also use the user\mods\DanW-LateToTheParty-#.#.#\db\LootRankingDataReader.exe program to view the ranking data and see how the key(s) compare to other items.

Regarding having loot despawned behind closed (or even worse, locked) doors, that is definitely an annoyance. Unfortunately, I haven't found a way of preventing it. I'll at least add it to the known-issues list, but it'll probably be very challenging to fix.

Let me know if you're still struggling with this even after playing with the config settings, and I can help you with more debugging to see what's going on.