Unity Collab not correctly saving files.

I am currently using version 2018.2.0f2.
I published a version using the unity collab tool on this build, 4 hours ago, I have just reverted back to this build to find a few things in my code broken, and some methods missing in a couple of my classes.
These classes where changed roughly end of November last so I'm not sure what happened, however I do know the changes must not have been recognised my unity.

EDIT: It looks like the files that didn't save were all moved between publishes

EDIT 2: According to another post, this was fixed in 2018.3

 

I've also realised after digging deeper, it has not saved some code from the publish 4 hours ago.

 

I've had the same issue recently with collab deciding to cancel a previous commit through a new one (previously added files were deleted and changes reverted to before. I also noticed some minor change on a prefab (a light moved) which I don't remember touching.

An other issue I have is some computers keep considering there has been changes on some assets even though we don't work on them. Reverting and deleting the collab library doesn't help.