I don't see the files listed as untracked in git status, and have even tried to modify one and it does show up as modified in git status, so the files are tracked. Why does git merge says they are untracked?
This is a git-annex repo if that matters.
$ git status
On branch master
Untracked files:
  (use "git add <file>..." to include in what will be committed)
    papiers/remcheck/
    "papiers/sant\303\251/"
    photos/android_arno_s10e.bak/
nothing added to commit but untracked files present (use "git add" to track)
$ git merge android_mj_dcim/master
error: The following untracked working tree files would be overwritten by merge:
    photos/android_pro_mj_new/.thumbnails/1598113434562.jpg
    photos/android_pro_mj_new/.thumbnails/1598163462676.jpg
    photos/android_pro_mj_new/.thumbnails/1598163519218.jpg
    [… edited for brevity]
Aborting
$ git ls-files --others --exclude-standard
papiers/remcheck/
"papiers/sant\303\251/Arnaud/DSC_0243.JPG"
"papiers/sant\303\251/Arnaud/DSC_0244.JPG"
photos/android_arno_s10e.bak/AR Emoji camera/20200413_094232.jpg
photos/android_arno_s10e.bak/AR Emoji camera/20200413_094331.jpg
[… other files from photos/android_arno_s10e.bak/ edited for brevity]