I had similar troubles in eclipse and the only way to fix it for me was to
- Remove the web module
- Apply
- Change the module version
- Add the module
- Configure (Further configuration available link at the bottom of the dialog)
- Apply
Just make sure you configure the web module before applying it as by default it will look for your web files in /WebContent/ and this is not what Maven project structure should be.
EDIT:
Here is a second way in case nothing else helps
- Exit eclipse, go to your project in the file system, then to .settings folder.
- Open the
org.eclipse.wst.common.project.facet.core.xml, make backup, and remove the web module entry. - You can also modify the web module version there, but again, no guarantees.