Even though this is an ancient thread, I'm replying because I had the same problem with Studio 2021 today and found a workaround that might help others.

Like Pablo, my problem was:

Some of the footnote tags (fn id) were not appearing in the SL column, even though the text of the corresponding footnote was appearing.

Interestingly, Studio clearly recognised these TUs as belonging to footnotes, because they appeared along with all the other footnote TUs when I set a filter to show me only footnotes.

I didn't even get to the stage of seeing whether the corresponding footnotes were missing in the translation after export, but I suspect they would have been.

Saving the Word file as .xml and looking at that in a text editor revealed that at least the first of the footnotes for which the fn id tag was missing in Studio had a whole bunch of xml tags associated with it that the others didn't. As it happened, this was Footnote 1. The "scientific" approach would have been to analyse all those xml tags, remove the ones that were causing a problem and then re-save the .xml file as .docx.

But life's too short. And what I know about xml could be written on a postage stamp.

So on a hunch, I deleted and re-created that first footnote as follows:

1. Opened the doc in Word
2. Copied the text of the footnote to the clipboard
3. Deleted the footnote marker
4. Created a new footnote at the appropriate location in the text
5. Pasted the text of the footnote into the new footnote as text (very important -- this trick did not work if I pasted the footnote text back in with its formatting intact)
6. Saved the doc
7. Imported it into Studio
8. Ran "Prepare"
9. Opened it

Most of the missing footnote tags now appeared -- not just Footnote 1, which I had re-created.

Of the 207 footnotes in my text, at least 50 had initially been missing their fn id tags. Now only three had that problem, so I just re-created those three as I had done for Footnote 1 and re-imported the document into Studio.

All of my footnotes now had tags!

From the fact that fixing Footnote 1 caused most of the other missing fn id tags to appear, I imagine that the code for Footnote 1 contains some "magic tags" that determine how Studio interprets the other footnotes as well, but that's just a wild guess.

Of course, this shouldn't be happening, but it does seem as if the "blame" is to be shared between Word (for messing up some of its footnotes) and Studio (for not coping with slightly corrupted or non-standard footnotes that work perfectly in Word).

Hope this is of use to some other sufferer at some point!