Please describe the problem.

Metadata are not stored in a consistent format. It seems more like git-annex chooses the "smallest" charset able to hold the data, i.e. US-ASCII, unless there are latin1 characters, and only UTF-8 if there are UTF-8 characters that are not in latin1

What steps will reproduce the problem?

% git init
Initialized empty Git repository in /home/madduck/.tmp/cdt.GlIevu/.git/

% git annex init
init  ok
(recording state in git...)

% date > a

% git annex add a
add a ok
(recording state in git...)

% git annex metadata -s one=$(echo US-ASCII | iconv -tus-ascii) a
metadata a 
  lastchanged=2016-09-25@13-18-57
  one=US-ASCII
  one-lastchanged=2016-09-25@13-18-57
ok
(recording state in git...)

% git annex metadata -s two=$(echo lätin1 | iconv -tlatin1) a
metadata a 
  lastchanged=2016-09-25@13-19-37
  one=US-ASCII
  one-lastchanged=2016-09-25@13-18-57
  two=lätin1
  two-lastchanged=2016-09-25@13-19-37
ok
(recording state in git...)

% git annex metadata -s three=$(echo unicode… | iconv -tutf8) a  
metadata a 
  lastchanged=2016-09-25@13-19-41
  one=US-ASCII
  one-lastchanged=2016-09-25@13-18-57
  three=unicode…
  three-lastchanged=2016-09-25@13-19-41
  two=lätin1
  two-lastchanged=2016-09-25@13-19-37
ok
(recording state in git...)

% git annex metadata -g three a | iconv -tutf8                 
unicode…

% git annex metadata -g two a | iconv -tutf8 
liconv: illegal input sequence at position 1

% git annex metadata -g one a | iconv -tutf8 
US-ASCII

% git annex metadata -g two a | iconv -flatin1 -tutf8 
lätin1

What version of git-annex are you using? On what operating system?

6.20160808-1