Some commands

Sync

If you want to sync one remote (probably a local path) to another:

rclone -v sync -P --filter-from .config/rclone/filter --delete-excluded /your/local/path <remote>:

See https://rclone.org/commands/rclone_sync/

Sync and backup modified files

If you want to sync one remote (probably a local path) to another.

And if you want to keep modified files (deleted, updated) in a backup directory:

rclone -v sync -P --filter-from .config/rclone/filter --backup-dir <remote>:/$(date +'%Y-%m-%d-%H-%M-%S') --delete-excluded /your/local/path <remote>:

See https://rclone.org/commands/rclone_sync/

Check two remotes

To check the consistency of two remotes (probably your local path and a remote):

rclone -v check -P --filter-from .config/rclone/filter /your/local/path <remote>:

It will use underlying features of the providers to do the check.
For example, for S3 compatible providers this means comparing the MD5 sum of your local files and the MD5 sum registered after the transfer.
But for Mega.nz, the check will only be based on the size of the files.

For encrypted remotes, use cryptcheck

See https://rclone.org/commands/rclone_check/

Check two remotes, at least one in encrypted

If you have an encrypted remote, you MUST use this command:

rclone -v cryptcheck -P --filter-from .config/rclone/filter /your/local/path <remote>:

See https://rclone.org/commands/rclone_cryptcheck/

ncdu

ncdu is a really usefull tool

And it has been implemented in Rclone 

rclone -v ncdu <remote>:

Rclone ncdu

See https://rclone.org/commands/rclone_ncdu/