Nothing of this seem related to JBT.
Projects available for deployment is simply listing WTP compatible projects and if mvn eclipse:eclipse is not doing it correctly then that explains it.
The maven guys have many time said that mvn eclipse:eclipse is broken and should not be used - use m2eclipse instead.
In any case, without having an example of projects that you say worked before but stopped working now I'm not sure what you want us to look at ?
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