Sorry, but we are not sure what you are trying to describe. We do not know what is wrong based on the information you have provided. We have no idea of how you are trying to update all of the different coordinate systems, since you seem to have many.
We suggest you get rid of any custom chart zoom class you might have and just used the regular default zooming. Try and get everything thing else to work. After a a day or two, if you can't get it to work, send us the simplest possible example program which reproduces the problem. That's all we can suggest at this time. Your program appears to be too complicated to fix by just talking about it.