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Translations strings become obsolete/commented out

I am in the process of translating Askbot in Greek. I am almost finished, I have already followed the relative instructions, but from time to time I get latest from askbot's repo, so I need again to run jinja2_makemessages to generate .po file including translation pairs for newly added messages. Particularly, in my local (windows) environment I run :

c:\askbot_work\askbot> python c:\askbot_work\askbot\myGreekProject\ jinja2_makemessages --no-wrap -l el -e html,py,txt

where askbot_work is my root folder (containing also the build folder), and myGreekProject is where lives and from there I run runserver.

Unfortunately, after this step, a lot of my pairs have got commented out like this

#~ msgid "by date"
#~ msgstr "ημερομηνία"

and all the meta information that appeared with the pair (like source file/line) has gone. This, of course, results a lot of messages appear again in English. I tried this but messages are still commented out.

As a workaround I just go and delete those #~ in the file, but I guess there must be a more proper, maintainable solution.

Thanks in advance!