Even in a newly created annex, git annex fsck fails.  Furthermore, the suggested solution apparently does not work.  Maybe the warning is simply spurious.  Does this occur in the latest release?

[[!format sh """
# If you can, paste a complete transcript of the problem occurring here.
# If the problem is with the git-annex assistant, paste in .git/annex/daemon.log

r0lf@work:/tmp/tmp$ dpkg -l git-annex
Desired=Unknown/Install/Remove/Purge/Hold
| Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
|/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
||/ Name           Version      Architecture Description
+++-==============-============-============-===============================================================
ii  git-annex      8.20200226-1 amd64        manage files with git, without checking their contents into git

r0lf@work:/tmp/tmp$ git init;git annex init
Initialized empty Git repository in /tmp/tmp/.git/
init  (scanning for unlocked files...)
ok
(recording state in git...)

r0lf@work:/tmp/tmp$ echo "test" > test.txt

r0lf@work:/tmp/tmp$ git annex add test.txt 
add test.txt 
ok                                
(recording state in git...)

r0lf@work:/tmp/tmp$ git commit -m "test commit"
[master (root-commit) d2e64c0] test commit
 1 file changed, 1 insertion(+)
 create mode 120000 test.txt

r0lf@work:/tmp/tmp$ git annex fsck test.txt 
fsck test.txt (checksum...) 
  test.txt: Can be upgraded to an improved key format. You can do so by running: git annex migrate --backend=SHA256E test.txt
ok
(recording state in git...)

r0lf@work:/tmp/tmp$ git annex migrate --backend=SHA256E test.txt
migrate test.txt (checksum...) (checksum...) ok
(recording state in git...)

r0lf@work:/tmp/tmp$ git annex fsck test.txt 
fsck test.txt (checksum...) 
  test.txt: Can be upgraded to an improved key format. You can do so by running: git annex migrate --backend=SHA256E test.txt
ok
(recording state in git...)

# End of transcript or log.
"""]]