I did that as well. I even created a new project, and tried running it with all the JREs installe don my system, but it just complains.
Actually I just found a workaround. I made a copy of the JRE tot he folder where the old one was, started Eclipse, and rechanged again all the LIbrary references to the new JRE. Then I closed it, deleted the folder with the "old JRE. After I started Eclipse, it didn't give me any problems. I guess it just likes to be "consulted first" when you're deleting a JRE from the system. Delete references to it in Eclipse, then you can uninstall it from your system.
[ December 22, 2004: Message edited by: Stan Smith ]