XWikiPreferences properties are not merged by the distribution wizard when previous version does not have properly installed extensions

Steps to reproduce:

• download a 2.7.2 jetty+hsqldb package
• modify the hibernate config to point to a MySQL or Postgres database
• add the according JDBC jar in lib
• start 2.7.2 and import the XAR
• stop the 2.7.2
• download the 4.3 RC1 from maven.xwiki.org
• unpack the 4.3-RC1 archive (in a folder, NOT over the previous installation of 2.7.2)
• delete the data/extension and data/jobs from the freshly unpacked 4.3-RC1 archive (needed in order to trigger the DW)
• configure your newly downloaded and unpacked XE instance to point to the same database you created earlier with 2.7.2
• make sure you use the Distribution Wizard to upgrade
• when you get merging conflicts, click on "Continue" and keep the default selected option (Keep new content, overwriting older/previous content)
• after a long and painful session of clicking the "Continue" button to solve merging conflicts, you will see that there is no Applications Panel.

Importing the XAR using the old way will make the Applications Panel visible.
Also, even if it is not displayed, the Applications panel is inside the Wiki.

Tested on MySQL and PostgreSQL