Rclone doesn't currently preserve the timestamps of directories. This is because rclone only really considers objects when syncing.
Currently rclone loads each directory entirely into memory before using it. Since each Rclone object takes 0.5k-1k of memory this can take a very long time and use an extremely large amount of memory.
Millions of files in a directory tend caused by software writing cloud storage (eg S3 buckets).
Bucket based remotes (eg S3/GCS/Swift/B2) do not have a concept of directories. Rclone therefore cannot create directories in them which means that empty directories on a bucket based remote will tend to disappear.
Some software creates empty keys ending in
/ as directory markers.
Rclone doesn't do this as it potentially creates more objects and
costs more. It may do in future (probably with a flag).
Bugs are stored in rclone's GitHub project: