The changes made for T6799: Kleopatra configuration files in wrong places have broken the migration of the group config because Kleopatra now looks in the wrong place for the old group config. Instead of looking in %LOCALAPPDATA% %APPDATA%/kleopatra Kleopatra now looks in %GNUPGHOME%/kleopatra for the old group config (which is also the new location).
This happens only on Windows (because we use %GNUPGHOME%/kleopatra only on Windows).
To test this move kleopatragroupsrc from %GNUPGHOME%/kleopatra to %LOCALAPPDATA% %APPDATA%/kleopatra. If migration works then Kleopatra will copy the group config file from %LOCALAPPDATA% %APPDATA%/kleopatra to %GNUPGHOME%/kleopatra.
Update (2025-07-15): When I created the ticket I erroneously assumed that older versions of Gpg4win had used %LOCALAPPDATA% for config files (including the group config file). That's not the case. Gpg4win 4.3 has used %APPDATA%/kleopatra for its config files (including the group config file). Note that migration of the group config files by VSD/GPD is covered by T7700: Kleopatra: Move kleopatrarc away from %LOCALAPPDATA%.