Lost previously created documents when migrating to 5.0.1 on HSQLDB

Steps to reproduce:

• Setup a standard XWiki 4.1.4 using Jetty + HSQLDB OR Tomcat + HSQLDB (I used Manager)
• Import the ui-all XAR

• create some pages in Sandbox page AND in a separate new space
• shutdown the wiki
• put the 5.0.1 WAR in Jetty or Tomcat + HSQLDB jar
• start the Wiki, use the DW to migrate.
• after the migration is finished your pages are gone. They are not even in the Deleted Documents page.

Reproduces from:
4.1.4 -> 5.0.1
3.5 -> 5.0.1
4.0 -> 5.0.1

Also tested on PostgreSQL and does NOT reproduce. This seems related to HSQLDB.