A couple of times the refactoring created rubbish in my JSP files. Formatting was destroyed, but much worse imports were ruined. Instead of being replaced fully with a new package name, the package name in the JSP after refactoring ended up being some mix of the old and new name. E.g. suppose the old name was com.java.foo and the new was com.java.bar, the name in the imports would be com.java.fobaro or something like that.
The last time I tried this was with MyEclipse 6.0, so maybe its better now.