One way around this is to force the AssetRegistry to rescan the directory:
TArray<FString> PathsToScan = TArray<FString>();
PathsToScan.Add(AssetDirectory);
const FAssetRegistryModule& AssetRegistryModule = FModuleManager::LoadModuleChecked<FAssetRegistryModule>("AssetRegistry");
AssetRegistryModule.Get().ScanPathsSynchronous(PathsToScan, true);
However, I am not sure if you are supposed to do that, somehow doesn’t feel right.