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Hi,
(In Trados Studio 2019 Pro SR1_For test). I intentionally omitted a tag (footnote tag) for a word in a target segment and confirm it. Then chose File | Save Target As. Trados Studio 2019 Pro, generated the translated document and I didn’t get any warning message in saving time!. The file I worked on it; is a .docx format that created in MS Word 2019. Also, I checked out Project Settings | File Types | Microsoft Word 2007-2016 features, but didn’t find anything for this, or maybe there’s something in there that I don’t know how to use it (check/uncheck options).
Best, 
Masoud
