How to make rsync to log deleted files

_{(Converted from question edit)}

This is solved by upgrading rsync. Version 3.1.1 or later will now replace identical files in the target and --link-dest directory with one hardlinked file. Saves lots of space.

Some suggestions for things to try come from the contents of the man page (the section about --delete). There are a lot of caveats and warnings. Have you considered all of these?

• Works only "for the directories that are being synchronized". I guess this means they must have a parent/ancestor directory being copied.

• Similarly, it doesn't apply to anything being explicitly excluded:

Files that are excluded from the transfer are also excluded from being deleted unless you use the --delete-excluded option or mark the rules as only matching on the sending side.

• If the sending side detects any I/O errors, then the deletion of any files at the destination will be automatically disabled. Override with --ignore-errors.

• Try with --dry-run first? Combine with --verbose and closely examine everything that's happening with problem directories.

  This option can be dangerous if used incorrectly! It is a very good idea to first try a run using the --dry-run option (-n) to see what files are going to be deleted.

So consider trying --delete-excluded, --ignore-errors, and/or --dry-run/--verbose...not necessarily as a "fix" but at the very least there may be helpful data to be gleaned.

Also, take a look at the --delete-before flag. This is supposed to do the receive-side deletes before the actual transfer. Again, this might not fix everything but could be revealing. It'd be interesting to see if it helps reduce disk space usage, too.