When you install the plugin it copies files to www/plugins and updates android.json
then when you build the project, the build copies the java to platforms/android/src/... and the js files to platforms\android\assets\www\plugins (and does any customisation defined in plugin.xml)
At multiple occasions I saw android.json not correctly updated and javascript files not copied. Removing and re-installing plugins solved the problem for me.
If you did not perform manual customisations to the platforms/android folder, I think the easiest way to clean your project would be to empty the /plugins folder and the platforms folder and then re-install all the plugins you need.