Nether portal linking issue

I play on a realm that was created before the nether update with full nether portal linking systems. We have built a new nether hub in the roof of the nether and we're having trouble linking the portals. All the portals that were linked after the nether update have relinked perfectly fine while the ones linked before have some issues. We try to link these portals to their new nether portals and we get teleported to completely unrelated portals, to portals that don't exist anymore, even to brand new portals hundreds of blocks away. Please help as I cannot find any resolution to this.