Due to class file redefinition working noticeably slower in the JDK5/6 JVM, the
tool can time out, deciding that the target JVM is dead, when attempting to
instrument a large number of classes at once. For example, if you start
Java2Demo in CPU profiling mode, and then try to change profiling to memory
mode, the tool will very likely close connection with the JVM after 1 minute or
so (standard timeout).

The solution is probably to check if method redefinition is happening on timeout
and if so, wait for more time. An alternative solution would be to redefine
classes in several portions, but that's harder to implement and may be dangerous
if some future kind of instrumentation really needs all (or some) of the classes
to be redefined "atomically", in one go.