I don't believe this has anything to do with the object being stored in Glacier. I just uploaded the same file to S3 standard and then downloaded via a threaded download. Here's how to reproduce with a file above the multi-thread-cutoff threshold.
- Upload
# rclone --config /root/rcs3/POC/config/rclone.conf --s3-shared-credentials-file /root/rcs3/POC/config/credentials --metadata --links --transfers 2 --checkers 32 --progress --include pero.scaff.fa.pac copy /pub/ppapadop/testdir s3-backup:testing
Transferred: 590.125 MiB / 590.125 MiB, 100%, 45.393 MiB/s, ETA 0s
Transferred: 1 / 1, 100%
Elapsed time: 13.3s
- Checking metadata on S3, Object is stored in standard. Other metadata is correct
# rclone --config /root/rcs3/POC/config/rclone.conf --s3-shared-credentials-file /root/rcs3/POC/config/credentials --metadata --links --transfers 2 --checkers 32 lsf --format "ptTM" s3-backup:testing
pero.scaff.fa.pac;2019-04-05 12:37:55;STANDARD;{"atime":"2023-06-09T11:34:03-07:00","btime":"2023-11-15T16:34:30Z","content-type":"application/octet-stream","gid":"1698224","mode":"100644","mtime":"2019-04-05T12:37:55-07:00","tier":"STANDARD","uid":"1698224"}
- Downloading file without multi-part-cutoff specified
# rclone --config /root/rcs3/POC/config/rclone.conf --s3-shared-credentials-file /root/rcs3/POC/config/credentials --metadata --links --transfers 2 --checkers 32 --include pero.scaff.fa.pac copy s3-backup:testing /tmp/ppapadop
- checking ownership (incorrect), should be ppapadop:ppapadop
# ls -l /tmp/ppapadop
total 604292
-rw-r--r-- 1 root root 618791129 Apr 5 2019 pero.scaff.fa.pac
drwxr-xr-x 2 root root 56 Nov 15 08:06 testdir
- Redoing by erasing local copy, downloading with the --multi-thread-cutoff 1024Mi and things are now correct
# rm /tmp/ppapadop/pero.scaff.fa.pac
rm: remove regular file '/tmp/ppapadop/pero.scaff.fa.pac'? y
# rclone --config /root/rcs3/POC/config/rclone.conf --s3-shared-credentials-file /root/rcs3/POC/config/credentials --metadata --links --transfers 2 --checkers 32 --multi-thread-cutoff 1024Mi --progress --include pero.scaff.fa.pac copy s3-backup:testing /tmp/ppapadop
Transferred: 590.125 MiB / 590.125 MiB, 100%, 14.972 MiB/s, ETA 0s
Transferred: 1 / 1, 100%
Elapsed time: 40.6s
# ls -l /tmp/ppapadop
total 604292
-rw-r--r-- 1 ppapadop ppapadop 618791129 Apr 5 2019 pero.scaff.fa.pac
drwxr-xr-x 2 root root 56 Nov 15 08:06 testdir