it might be helpful to use ent who on some building blocks. they should always say 0 and if they don't then this might explain why this happens. otherwise I don't know without some way to reproduce it.
Despawn Dropped Loot Bags From Raid Boxes When Base Despawns, this is in the profiles (oxide/data/RaidableBases/Profiles/) and I had people enable this as a workaround before. if this still works then let me know
the log file option, Log Debug To File is useless. it always says the base was despawned when it wasn't. that means the despawn was called but it didn't work for whatever reason.
server log might be helpful. if you don't know what a server log is then have your host help you find it or enable it if it's not enabled. logs are sometimes called log.txt, server.log, latest.log, and may be found in root server folder, /logs/2023/07/20/ for example. if you don't see any of those then your host must help you to enable it.
these are not server logs. anything with oxide in the filename is not a server log either.