I backed up my Mac with Time Machine, erased the drive, and reinstalled 10.14.4 from USB. After the install process was complete, I restored my data from the Time Machine backup I had made a couple hours prior. The only issue is that I seem to be missing that two hours worth of messages (which were received/responded on my iPhone); there's a two hour gap of messages missing on my Mac.
I can send/receive messages from my Mac post-reinstall just fine, and I see all the messages in various threads exactly as they were while the computer was being backed up via Time Machine. 'Enable Messages in iCloud' is enabled, and was enabled before/after this process. I still have a two hour gap in messages on my Mac though - my iPhone contains the complete list of messages.
Has anyone else encountered this? I would have hoped that iCloud would have noticed the missing messages on the Mac, but that doesn't seem to be the case. Restarting a few times/keeping iMessage open for over an hour doesn't seem to invoke it to sync the missing messages either.