Hello Emma Starr

Thank you for your clear findings. I did take a quick look through our internal support channels/platforms to see if this is an issue felt by the wider community around IDML footnotes. It does not seem to be the case.
There were improvements made in SDL Trados 2017 but I assume you are working on a new version of the tool. Can you please confirm?

Regardless I clearly see your concerns as you describe them, but without your files I am unable to give a resolution.

Is it possible to send some without compromising any data security?
I assume your missing footnotes is isolated to this particular file?
Do you have it working in other examples?

Historically I would explore the formatting around the footnote within the native source document.
Check the missing footnote is somehow different from those examples where it is working.

What I also find insightful to try understand what Studio has done by processing your file. I do this by changing the view from all segments to all content. All be it a poor example we can see some gaps between the segments. In my case between 151 and 152.

At times there can be valuable data in there, such as your missing text wrapped in tags. All be it we can’t access it for translation, it does help confirm the root cause and what could be our next steps in correcting the way your content is being processed. 

Looking forward to your confirmation to my questions and if possible your files

Regards

Lydia