You can't use a partial refresh in conjunction with a file upload control as you can't currently post a file to the server during this process.
Also what you mentioned about using a partial refresh without a target sounds very strange. A partial refresh is designed to refresh an area without touching the rest of the page, if you have multiple areas that can't be grouped in a panel or something like that you should either use script to refresh these sections or if there is many of them it sounds like it might be best to do a full refresh.
on a side note it sounds like what your doing in the refreshes is hiding / showing these controls. calling " getComponent(<id>).setRendered(true / false); " sounds like a much better solution than refreshing the page to compute one or two render properties.