There can't be a direct problem related to class - loading when using different full - qualified - classnames. There can be issues, though, with CDI.
Remember that Inject can be applied to many Resources, and the injection target can have the type of an interface rather then having the type of the implementing class.
When determinating on which object is to be instanciated, the application server /CDI container could run into problems when suddenly there may be more implementations of that interface available after a deployment then before, e.g. both annotated with the same or default qualifier, though a exception is expected here rather then a random injecting of one class or the other.