So I tried it today and it turns out that everything works perfectly. The mistake I did was that the first time I did 'svn up --ignore-externals user' and I forgot about the --ignore-externals parameter so the next time ('svn up' in 'software') naturally the externals (for 'user') were fetched as well (I should have paid more attention to the file names!).
So no regression, only a silly user. Thanks for your amazing work, guys. Regards, Miro