Thanks for reporting. References are often supported by templates which are created independently on each wiki, and the process of finding equivalent templates and parameters is not trivial. However, in this case the problematic references do not seem to use a tempalte. They just have a ref element that should be copied over. Can you confirm these are some of the references that disappeared?

<ref>Dissertation: ''Individualisierungsprobleme der Teilleistungsklage''.</ref>

<ref>[http://www.spiegel.de/schulspiegel/wissen/0,1518,491434,00.html Mit der Bibel in den Biologie-Unterricht? spiegel.de, 29. Juli 2007], abgerufen am 5. Juni 2012.</ref>

<ref>[https://www.welt.de/politik/article1006014/CSU-Politiker-unterstuetzt-Wolffs-Bio-Schoepfungslehre.html Kreationismus-CSU-Politiker unterstützt Wolffs Bio-Schöpfungslehre welt.de, 7. Juli 2007], abgerufen am 5. Juni 2012.</ref>

That is correct. This is the version I was translating: https://de.wikipedia.org/w/index.php?title=Christean_Wagner&oldid=202808312 . I believe I was trying to preserve all references in this case (as in: I don't believe I removed them myself in the editing process before saving them).

As a sidenote: I realize that templates make life harder, but I would still expect the system not to fail silently, but to rather alert me that something did not get transferred, and show me what its content was. That could be by introducing an 'ugly' version of the template text in the new article, by introducing an error, or some more user friendly way during the translation process.

In T261170#6532817, @Effeietsanders wrote:

That is correct. This is the version I was translating: https://de.wikipedia.org/w/index.php?title=Christean_Wagner&oldid=202808312 . I believe I was trying to preserve all references in this case (as in: I don't believe I removed them myself in the editing process before saving them).

Thanks for confirming

As a sidenote: I realize that templates make life harder, but I would still expect the system not to fail silently, but to rather alert me that something did not get transferred, and show me what its content was. That could be by introducing an 'ugly' version of the template text in the new article, by introducing an error, or some more user friendly way during the translation process.

A warning message is shown, but that may fail in some cases. For in-line templates the context is added. However, we try to be careful with adding incomplete/broken templates since that generates work for the editing community if those go unnoticed by the translator.

The intended solution is to show the missing references in grey to communicate they need information but avoid publishing if they remain incomplete (this is described in more detail in T203160). There may be some issue in that logic leading to the problem described in the ticket (references silently disappearing).