For example if a module depends on Apache Commons Collections:

When using "Reload in Target Platform", the jarfile passed to the CLI is the file located in "target/", but in the manifest file of the jar, the dependencies are listed like:
X-Class-Path: ext/commons-collections/commons-collections-3.2.1.jar
Maven-Class-Path: commons-collections:commons-collections:3.2.1

But the file doesn't exist there, so you get ClassNotFoundException when trying to use classes from that library.

Instead, if target/nbm/netbeans/[name]/modules/[modulename].jar is used, then the ext folder with the dependencies are present, and the manifest has this instead:
Class-Path: ext/commons-collections/commons-collections-3.2.1.jar

Easy way to reproduce:
* Create  a new maven netbeans application
* create a new maven netbeans module
* Add commons collections as a dependency to module
* Create an action that uses a class from that library for instance: JOptionPane.showMessageDialog(null, new org.apache.commons.collections.bag.HashBag().getClass().toString());
* Start Application
* Trigger action -> popup box with "class org.apache.commons.collections.bag.HashBag"
* Select "Reload in target platform"
* Trigger action -> java.lang.ClassNotFoundException: org.apache.commons.collections.bag.HashBag

For Javeleon usage, we are currently patching the binaries in JaveleonModuleReloader to reload from target/nbm/netbeans/[name]/modules/[modulename].jar, but for standard module reloading the problem remains.