Sorry if this explanation rambles a bit but I just had shoulder surgery this morning and am on the "good" stuff
Clearing the cache should not effect cookies in any way. My browser cache is cleared automatically every week as part of my backup process and I've never had a problem. Some browsers do default to clearing both the page cache and cookies, but you should be able to control that through the "Tools" menu on your browser. After clearing cookies, it may take a couple of tries to log in as the site remembers you, requests your cookie so it can log you in, and times out if your browser doesn't reply or sends a null value. I'll take a look at the code and see if there is anything we can do to make it work better.
Java is used to provide extended functionality for HTML on the site. I have been converting routines to php because it is faster and more flexible but am not sure how much Java is still around. I'll check and see if we can do away with the Java requirement.