The meta-data are saved in the system when you upload your respondents files (see "Through mail merge" for more information). Therefore, they remain clearly separated from the responses given by your responsents. If you upload 2 different files with different emails and containing different meta-data, all the meta-data will be able to be analysed. If you upload 2 different files with the same email adresses and containing different values for the same meta-data, only the last upload will be taken into consideration.
You can, at any time, delete the respondents file. But by doing so, you will also delete the corresponding meta-data as well as their related analyses.