As a sample, I tried to align a project containing OmegaT's Bundle.properties against Bundle_fr.properties
Let's consider the entry MW_REOPEN_QUESTION
MW_REOPEN_QUESTION=OmegaT needs to reload the project to take the modifications into account.\n\
Reload the project now?
and
MW_REOPEN_QUESTION=OmegaT doit recharger le projet pour prendre les modifications en compte.\nSouhaitez-vous recharger le projet maintenant ?
In the file align.tmx file I see this:
<tu>
<tuv lang="en-US">
<seg>In order for the changes to take effect OmegaT needs to close and then open the project.
Reopen the project now?</seg>
</tuv>
<tuv lang="fr">
<seg>Souhaitez-vous recharger le projet ?</seg>
</tuv>
</tu>
The source contains two phrases, but from the target, only the last phrase was kept.
I see two potential expected results.
Solution 1: align by paragraphs
<tu>
<tuv lang="en-US">
<seg>In order for the changes to take effect OmegaT needs to close and then open the project.
Reopen the project now?</seg>
</tuv>
<tuv lang="fr">
<seg>Pour mettre en application vos modifications, vous devez fermer puis recharger le projet. Souhaitez-vous recharger le projet ?</seg>
</tuv>
</tu>
Solution 2: align by segments
<tu>
<tuv lang="en-US">
<seg>In order for the changes to take effect OmegaT needs to close and then open the project.</seg>
</tuv>
<tuv lang="fr">
<seg>Pour mettre en application vos modifications, vous devez fermer puis recharger le projet</seg>
</tuv>
</tu>
<tu>
<tuv lang="en-US">
<seg>Reopen the project now?</seg>
</tuv>
<tuv lang="fr">
<seg>Souhaitez-vous recharger le projet ?</seg>
</tuv>
</tu>
I let you decide which solution you prefer, whenever it should be an option, etc. But actual behavior is clearly not correct.
Diff: