Customized modules translation

[superautomatic]

I'm building a prestashop site with a lot of modules customized by copying the modules folder and .tpl files to /themes/mytheme/modules (to not mess with the original). One thing that does NOT work with this approach is the translation of the modules. When the modules resides in the /themes/mytheme/modules directory, each time I update a translation in the backend a new, empty languagefile is written to the customized folder. For example, in my copy of blockcart an empty se.php (for swedish) is created, overriding the correct (and updated!) one in the original modules/blockcart folder. The only way to solve this is by manually deleting all the empty language files created in the custom module directories every time a translation is updated.
Any ideas on how to solve this (really annoying) problem?