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This is what I'm seeing ...
Clearly a terrible user experience and for that I'm sorry. It is fixed and the next patch will clear up the chatty error messages related to /.svn/ folders.
Still I don't lose a file so perhaps there is specific series of events...?
I'm also use Versions instead of subclipse so going to download Eclipse and subclipse when I get to get internet.
Sencha Architect Development Team