I figured this out after a confusing incident where OmniWeb hung at launch after updating to the latest build, but rolling back to an older build and restoring the ~/Library/Containers/com.omnigroup.OmniWeb6 folder from a time machine backup failed to fix the problem.
A completely new com.omnigroup.OmniWeb6 did fix the hang, so I narrowed it down file by file until Favorites.html was implicated. Then I bisected the entries inside it until it turned out the problem was being caused by one entry having the attribute “status=unviewed”.