When you update custom variables on a survey, they take precedence over custom variables uploaded along with the email address. So if you pass / upload custom variable along with the email address as custom variable 1 "${custom1}" and the same custom variable 1 is updated midway in the survey, then the value passed via the email address will be lost.
Make sure you are not updating the same Custom Variable in two different questions. The latest information will get updated to the Custom Variable overwriting the text that earlier existed in Custom Variable.
Please make sure you test the survey and also check how the responses are saved before making the survey live.