Further tests have shown that the bug in flexbackup seems to surface only when using tar. I did not test all other tools supported by tar but several backups using cpio and zip all went through without the problem. Debian Jessie used tar 1.27 while Debian Stretch uses tar 1.29. I can't tell if the problem exists because there was a change in the way tar parses its input or commands or if there is a problem in tar itself. Maybe somebody who is better than me looking at “long command lines” (do flexbackup ... -n to make a dry run and see the command line) can tell what is wrong.

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