no it doesn't. Skins used by the site are under /Data/Sites/[SiteID]/skins and we don't update anything in that folder.
new skins or updated skins will be in /Data/skins but if you want to use any of them you would have to copy them manually from /Data/skins into /Data/Sites/[SiteID]/skins
no user uploaded files will be touched at all, only files included with previous versions of mojoPortal will be updated, when you upload the/Data folder it will not replace the existing Data folder it will merge them and would replace any files that have the same name and location but other files will not be touched
of course it is always a good precaution to backup all the files first but there should be no lost files
Hope that helps,