Description:
Testing using Thresher and 2nd release of AJAX components.
Likely this works for any component, but I have not tried it.

Steps:
drop a progress bar
double click it
> this takes you to the Java editor
edit undo
click on the edit menu again
> notice no more undos are possible

switch back to design view
> the action property for the progress bar is still bound to a new event method

Evaluation:
This is a known issue. You should be able to reproduce the same problem with a 
Button also. In the current implementation, undo doesn't span .java and .jsp. 
You will have to do undo on .jsp separately to remove the code

Evaluation (Entry 2):
The behaviour is expected as per current design, therefore changing it to RFE

Workaround:
Switch to JSP view and do the undo