Most of the information is stored in the Tiki database (things like user preferences and Wiki page text content) so that won't get replaced by installing files. However, just for safety's sake you might want to backup any directories where you save files to, for example, file galleries, wiki attachments, forum attachments etc. The can also be stored in the database too, although this can then result in a huge database, so generally speaking it's preferable to stores these in directories.
In any case, whatever method you choose, you should always be backing up your data, be it database or files. That way you can guarantee nothing will be irrecoverably lost.y