I loaded Atazanavir on Spanish Wikipedia into CTX and added the first three paragraphs. You will notice all the references are in place.
I made no other changes as I was testing this tool as some of my volunteers were having issues. Than when I hit publish I get the following with the references missing from the first two paragraphs. Also the Wikipedia page " HIV/AIDS" ends up as " #sida/de VIH "
Details to reproduce the issue
The example is a reference that is used in multiple parts of a paragraph. All those instances appear in Content Translation when the paragraphs are added to the translation. But some of them are lost after publishing.
In Content Translation:
The red circles show the places where the reference "" was expected to appear but failed to do so.