As a practical matter it is likely to break somebody's unit tests.
If there's an alternative approach that you want people to use in their unit tests, go ahead and break it. If there isn't, but you're only doing such breakage rarely and it's reasonable for their unit tests to be updated in a way that works with both versions of your library, do it cautiously. Otherwise, only do it if you own the universe and you hate future debuggers.
Stop reinventing the wheel.
Major translation systems like gettext (especially the GNU variant) have decades of tooling built up for "merging" and all sorts of other operations.
Even if you don't want to use their binary format at runtime, their tooling is still worth it.