A few document fields are not taken into account when doing a 3 ways merge

I've upgraded a subwiki on myxwiki.org and once the upgrade was finished I noticed that the hidden documents are not hidden...

Some details:

• Upgrade from 3.5 to 5.0 (I repaired the install and mentioned it was a 3.5)
• A page I checked that should have had the hidden flag set is AnnotationCode.WebHome
• This page didn't have any merge conflict during the upgrade
• This page doesn't have the hidden flag set in 3.5