Onedrive gateway timeout error

hello and welcome to the forum,

those flags should not affect rclone lsf, as that list files, does not transfer them,

and from that link you shared

so i think your command should have been
rclone lsf --onedrive-list-chunk, not rclone lsf --onedrive-chunk-size

as a test, i might create a new dir and copy the files into the new dir.
and then run rclone ls on that new dir.
and if that works, try rclone copy/sync