Updating from koffice to calligra the way the koffice mask comment advises, I encountered a bunch of file collisions for app-office/calligra-l10n. Apparently portage wanted to first merge calligra-l10n, then unmerge parts of the koffice-meta stuff, and finally merge calligra itself. So koffice was still around while calligra-l10n was due to be merged. To fix this, I suggest you have the calligra-l10n ebuild block app-office/koffice-l10n, as that is where the conflicting files apparently come from.
Fixed in main tree, thanks for the report.