Sync copies everything

Sorry for the delay.

Here's the config I use for the test:

{
  "scaleway": {
    "access_key_id": "<redacted>",
    "acl": "private",
    "bucket_acl": "private",
    "endpoint": "https://s3.nl-ams.scw.cloud",
    "env_auth": "false",
    "location_constraint": "nl-ams",
    "provider": "Other",
    "region": "nl-ams",
    "secret_access_key": "<redacted>",
    "type": "s3"
  },
  "scaleway-encrypted-bucket": {
    "directory_name_encryption": "true",
    "filename_encryption": "standard",
    "password": "<redacted>",
    "remote": "scaleway:klingtnet-rclone-test-bucket",
    "type": "crypt"
  }
}

As test data I used rclone's git repository, i.e. ./some/local/folder will be ./rclone and headphone will be replaced by README.md. Here's the script, based on the commands you suggested:

#!/usr/bin/env bash

ls -al ./rclone | grep README.md
rclone lsl ./rclone | grep README.md
rclone lsl scaleway:klingtnet-rclone-test-bucket
rclone touch scaleway:klingtnet-rclone-test-bucket/testfileplain
rclone lsl scaleway:klingtnet-rclone-test-bucket
rclone lsl scaleway-encrypted-bucket:
rclone touch scaleway-encrypted-bucket:testfilecrypt
rclone lsl scaleway-encrypted-bucket:
rclone lsl scaleway:klingtnet-rclone-test-bucket

This is the output of test.sh:

$ bash -x test.sh 2>&1 | tee test.log
+ ls -al ./rclone
+ grep README.md
-rw-r--r--  1 alinz alinz    6361 Jul  4 13:32 README.md
+ rclone lsl ./rclone
+ grep README.md
     6361 2021-07-04 13:32:23.370319455 README.md
     3765 2021-07-04 13:32:23.403647128 docs/README.md
     3119 2021-07-04 13:32:23.473635240 librclone/README.md
      167 2021-07-04 13:32:23.466969707 graphics/logo/README.md
     1063 2021-07-04 13:32:23.430309266 fstest/testserver/init.d/README.md
      929 2021-07-04 13:32:23.430309266 fstest/testserver/images/test-hdfs/README.md
      346 2021-07-04 13:32:23.430309266 fstest/testserver/images/test-sftp-openssh/README.md
      853 2021-07-04 13:32:23.426976498 fs/rc/js/README.md
+ rclone lsl scaleway:klingtnet-rclone-test-bucket
        0 2021-07-04 13:55:34.215055494 testfileplain
       32 2021-07-04 13:53:55.641436814 tq5tg8hr3ffiurfq210hf3up8o
+ rclone touch scaleway:klingtnet-rclone-test-bucket/testfileplain
+ rclone lsl scaleway:klingtnet-rclone-test-bucket
        0 2021-07-04 13:55:38.003782142 testfileplain
       32 2021-07-04 13:53:55.641436814 tq5tg8hr3ffiurfq210hf3up8o
+ rclone lsl scaleway-encrypted-bucket:
        0 2021-07-04 13:53:55.641436814 testfilecrypt
+ rclone touch scaleway-encrypted-bucket:testfilecrypt
+ rclone lsl scaleway-encrypted-bucket:
        0 2021-07-04 13:55:40.287158304 testfilecrypt
+ rclone lsl scaleway:klingtnet-rclone-test-bucket
        0 2021-07-04 13:55:38.003782142 testfileplain
       32 2021-07-04 13:55:40.287158304 tq5tg8hr3ffiurfq210hf3up8o