I generally download responses periodically when running surveys, just to be on the save side. Should be something wrong with the installation, at least I have the old ones. Depending on the daily number of responses I do that daily or every two days or every week or something. It doesn't take too much time, because usually you follow the field anyway, but it saves you from these kind of things. Also, whenever I clean anything in the system, I generally download a dataset and just archive it. Should something happen like you described, at least you have it in Excel or CSV and can include it in the final data set if necessary.
Of course this is too late now for you, but maybe for the future worth for consideration. Maybe I am a little paranoid, but it doesn't take much time and doesn't hurt to have several versions of the responses downloaded. Just make sure that you are not getting confused which is the latest one.
I answer at the LimeSurvey forum in my spare time, I'm not a LimeSurvey GmbH employee.
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