Hello,
perdon for the delay, but the Covid is not a sympatical illness. :-(
I have just finished the test of encfs with the older rsync's version 
(3.1.2-2.1) on a virtual machine. The problem (IO error encountered -- skipping 
file deletion) is still there, so it looks like there is no bug with rsync. I 
don't know why there is this new problem on my machine, but it is not because 
of the new version of rsync. So, I think we can close the report.
Thank you very much for your help and attention and sorry for wasting time.
Claude MICOUIN

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https://bugs.launchpad.net/bugs/1955347

Title:
  rsync works bad with encfs now

Status in rsync package in Ubuntu:
  Incomplete

Bug description:
  Hello,
  I think rsync works bad with encfs now.

  When root uses it, rsync cannot read a directory encrypted with encfs
  by a user. More precisely, it cannot read the mounted directory, the
  virtual one where the user can read the datas.

  Until now there was only a warning like this
  "rsync: readlink_stat("/home/claude/Documents_chiffres") failed:
  Permission denied (13)"
  and the software went on working (only ignoring the content of the mounted 
directory and of course without saving this content)

  But recently there is this more:
  "IO error encountered -- skipping file deletion"
  and because of this "skipping file deletion", the software can't work 
normally. The destination gets bigger more and more because the deleted files 
in the source are not deleted in the destination.

  Thanks for reading me.
  rsync 3.1.3-8ubuntu0.1
  Description:    Ubuntu 20.04.3 LTS
  Release:        20.04

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