OK. You just bought 1password 4 for iOS and downloaded it to your iPad or iPhone. You set it up and confirmed all the data is there and now you want to delete 1Password 3, right? But you got an error that says "Deleting "1Password" will also delete all of it's data" and now you don't want to tap delete and later find out that it's deleted all the data from dropbox and it's going to be a big pain in the but to get it all back? Fear not, you can delete it and your 1password 2 app and the dropbox data will be unaffected.
What the iPad or iPhone is talking about when it says "Deleting "1Password" will also delete all of it's data" are two things: 1) 1passwords application data 2) User files associated/packaged with the app. In the case of 1Password, the dropbox file is not part of the user associated files save with 1password app because it is stored outside of 1password (in Dropbox). The data that iOS is warning you about are those files which might be wrapped up with the app. In this case, you can safely delete 1Password 3 because and files in dropbox will remain untouched.