The .ts files are XML files, so you could merge them with a text editor and maybe use or diff and patch commands (i'm not into unix enough to help out more).
But the problem is there, even if you "just" upgrade to a new version of ezPublish, you could loose your custom translations. I guess, this should be solved by some kind of override mechanism, as it is done with the .ini files (needs coding from ez).
I believe that the problem that raises Cristian is but on the posibility in which the translations with the file are being made at the moment translation.ts.
I explain, if we try to use translations in sections or in design texts for each site there's not a posibility to make it since all the translations depend on one or several files placed in share (common directory for all site's of ezpublish).
