You do not quite understand what you are actually doing, I will try to guess (next time, please provide more detailed information if you want help).
I assume that you created the cordova 3.x project using cli, added the Android platform and then imported the platform / android project into eclipse (at this point I hope that you did not check the “copy projects into the workspace” option).
Then you modify the html / javascript files in the projectroot / www folder, and these changes are not reflected when you go into eclipse and create apk.
Sorry if my assumption is wrong, but if it is not, I think you are missing a step in the process.
Here's what you should do (if you created the project using phonegap cli and not cordova, replace cordova with phone entries in the following command):
- make changes to the projectroot / www folder
- run the
cordova prepare android command - go to eclipse and update the project
- build apk in eclipse
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