this looks something strange, can you try exporting data in legacy format if you are exporting same to tabular or vice versa.
I would contact support- that feels like a technical error they should be aware of. I've never seen anything like that.
My "have you tried turning it off and back on again?" solution that seems to solve a lot of such issues is to refresh your account. Give that a go and try to re-download. But TBH this is not a bullet-proof solution, just a quick thing to try.
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While you wait for help from Support I suggest you download as numeric values since you said that is working. Then you can highlight the questions which you want to replace with value labels and run a find and replace in Excel. For instance, a condition of your find and replace might be: Find 1, Match exact cell contents, Replace "no effect". You can go into the survey editor, and look at the
recode values setting to make sure you are matching the correct number with the correct label.