We tried uninstalling the site and re-installing and while it fixed the primary site problems it badly messed up the syncing with the central site.
In the end we followed the process below:
- Revert the primary site to a central site
- On the Central Site run:
Preinst /delsite SiteCode ParentSite
Preinst /deljob SiteCode - On the old Primary site run:
Preinst /deljob SiteCode - Convert the old Primary site back to a primary site with the Central as it's parent
- Run Preinst /keyforchild on the central site and copy to \inboxes\hman.box
- Run Preinst /keyforparent on the primary site and copy to \inboxes\hman.box
- Run Preinst /Syncchild:SiteCode on the Central Site
- Run Preinst /syncparent on the primary site
This thankfully brought our sites back to life.
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