All strong holds have no end portals

we recently started a new realm when the cliff and cave update two came out. We found a stronghold on survival and it had no end portal inside. It looks like the caves have over written the strong hold. I made a copy of the world to check for any other. Strong holds and portals. I found 3 strong holds and NON of them have a portal inside. This is ridiculously frustrating as we can not progress our realm without one. The only option I have is to switch on cheats and I build a portal, however this will cause us to loose achievements. I now have 15 players screaming at me to fix the portal problem.