usryjw,
Can you please try these steps ?
a) There is file “org.eclipse.wst.common.project.facet.core.xml” in “.settings” directory of the project (which is hidden).
b) Edit the file and remove entry:
<installed facet=”project facet com.ibm.websphere.extended.ejb” version=”xxx”/>
c) Remove each troublesome entry
as it might be more than just “com.ibm.websphere.extended.ejb” facet and save the file.
This should fix the issue. Let me know how it works for you.