Viruses in the Linux world are, for all practical matters, non-existent. Unless you have valid reasons to believe that the Ubuntu machine you're going to use has been tampered with to destroy data in devices inserted in USB ports, you haven't nothing to worry about.

However, from your question it looks like (I might be wrong) you haven't any backup of the data files. If this is the case, you should do that ASAP: files can be damaged not only by viruses but also by disk crashes or human errors, such as deleting the wrong directory.