I have added the test over at: https://source.jboss.org/browse/~raw,r=42846/JBossTools/trunk/as/tests/org.jboss.tools.as.test.core/src/org/jboss/tools/as/test/core/parametized/server/publishing/defect/PublishWeb2DeletesWeb1LibsTest.java
THe test imports the 5 projects with the structure you mentioned above. IT adds them to the server one by one, executing a full publish each time. It then verifies the new module publishes properly with its libs, and also, that the previouspublished modules libs still exist.
The unit test fails to replicate your issue.