Repair phase is not executed nor prompted on subwikis when Upgrade All Wikis option is selected from DW

Steps to reproduce:

• setup a 4.1.4 XEM (I used TOmcat + MySQL)
• manually import the manager-ui-all.xar (since there is no DW on this version)
• install workspaces template
• create a workspace
• shudown and replace the war with a XE 5.2.2-SNAPSHOT (we only have the XE war since we don't build XEM anymore)
• start and DW kicks in
• from the DW, select that "This is an upgrade", and select 4.1.4 as the current version
• the repair step kicks in (for the main wiki). Click on Repair, this will upgrade the main wiki.
• after the main wiki is upgraded, for the rest of the wikis select "Upgrade All Wikis"
• starting to upgrade the other wikis (I started with workspaces template) I got a ton of merge conflicts. Same for the workspace I created earlier.

It seems that the repair phase only executes on the Main wiki.