Its funny how many religious help answers there is in this thread.
Log out/log in from messages. (classic Windows solution)
Reboot the device.
Use DiskUtility. (maybe Apple should use a better file system? Especially people using HSF+: surveys show that 90% of the users have rights errors that are created by the file system). macOS is Unix. The best OS in the world that is used on all high-end servers/mission critical stuff. Rights issues on file system should not exist and have been addressed a bit by APFS. (even if Apple forgot read/write verification).
This issue is activated by pressing "sync with icloud" = the whole point with messages in the cloud. (and every single Mac user I know moved their messages to iCloud to fix the simple issue that Apple cant propagate the same data to users with many Apple devices. The desperate theory is that if it's on the cloud= at least syncing this data should be easy. And every single one of these users pays for extra iCloud space, so messages in the cloud is a pay service that does not work.
I have no idea how to solve this problem. If I log out/in messages macOS. Tim thinks I only have SMS messages, every single imessage thread is gone. If I write to a user with messages, that thread is activated when the messages are sent. So I could try to send a message to every single person I sent a message to the last 5 years to repopulate the list. But... Tim thinks that is bad since when I quit messages and start it again he forgets all threads.
diskutil, log in/out. Read backups from TimeCapsule. Play with the lib folder. Reset PRAM. Pray to Tim. Nothing worked. heck.. Maybe I should threaten macOS that I will install Windows over it... oh... Tim has removed bootcamp in 10.14 = why that threat does not work.
How hard is it to sync data peer to peer? If I have 5 Apple devices: why can't they have the same messages data? iSync managed this and solved sync issues by asking the user what version should be saved (and making it easy for customers is one of the reasons why this does not work today. Sync conflicts aren't solved)
Since all macOS 10.14 machines are affected: how can it be a local error?
And it works on 10.13 machine that I have not upgraded yet. So maybe someone at Apple should fix this? Be a hero to its users that love their products because "they work"? (I miss Steve. When @me launched and you could not log in the first day: he summoned the cloud team in the auditorium. Took the boss to the stage. Said: You have failed each one of them (engineers/customers) and fired him. As a user, I got 2 years free @me just because of slow logins.
With Tim and the disaster iCloud/macOS: They can do anything. Manhandle the users. And nothing never happens since it works for Tim. Tim has a local icloud server hub under his desk with 10Gbps dual ethernet. "it works for me". That is today's Apple. Someone should be fired for this messages bug, especially that it was not fixed with 10.14.1