If you start Wildfly with all modules enabled and started.

Now use STOP action on an EAR module.
Now stop Wildfly.
Now start Wildfly (debug or run).

It will start up without the EAR module running, this is correct behavior at this point.

Now use START on EAR module. It fails to start at all.

This is because the file *.undeployed still exists. If you manually remove the file (using system file manager) the module will start up.

If you perform a "full publish" on the module that appears to cause it to start up as well.