The FAQ for conditional fields states "Conditional Fields are only displayed if another field meets a defined test. This allows you to build complex forms that hide fields that do not need to be filled in based on the answers to other questions." This explanation makes perfect sense and conditional fields indeed are hidden if the logical condition is met. Unfortunately, the contents of the conditional field are erased if the field is hidden, which is unexpected and undesirable behavior.
Let me illustrate with a shopping list, which contains checkboxes for a long list of things to buy. Suppose I'm a very well organized shopper, and I make the fields for each department in the store be conditional on a checkbox for that department. So I go through the Produce department, and click on the checkboxes when I'm picked up the carrots, lettuce, ... Once I'm done in the Produce department, I click on the Produce checkbox, which then hides the individual checkboxes for all the things that I just bought in the produce department. This means that I don't have to scan through all those checked items when shopping in other departments. That's just the behavior that I wanted.
But that night, while cooking dinner, I discover that we have no carrots. My wife gives me a hard time about how Mr. Uber-organized shopper could forget the carrots. So I pull out the checklist and uncheck the "Produce" box, so I can show her that I had checked off the carrots, and... AAARGH! All the checkboxes that are conditional on the Produce field are no longer checked.
Also, If I then email the results of my checklist to Mom, to show off what a well-organized shopper I am, all she sees is that I checked off the Produce box. What I really wanted was for her to see that I am diligently eating my carrots, but she just sees that I shopped for Produce.
IMHO, conditional fields should control only the *display* of the form, but not affect the contents.