When doing a Refactor > Encapsulate Fields > Do
Refactoring when you have asked to add getter and
setter accessors, the IDE should also generate the
javadoc automatically for the getter and setter
methods, especially if there public getter and
setter accessors. It might also make sense to have
a checkbox in the output window identifying that
it will udpate the javadoc for getter / setter
accessors. In addition, if you undo the
Refactoring, it should also undo the javadoc update.

Currently, the javadoc for a refactoring using
Encapsulate Fields does not change the
affected method's javadoc automatically. You have
to do it in a separate command or do it manually.

See a related issue: 
53147 "Automatically update javadoc on Change
Method Parameters > Do Refactoing"