As Jeremy briefly noted in his news roundup, yesterday, there was some concern that the latest Windows 10 update could be causing some users to lose files. These concerns have not been confirmed by Microsoft. They have started to investigate it, however.
Until they know that there is an issue (and, if so, have developed a fix for it) they are suspending the rollout of the Windows 10 version 1809 update. They are also recommending the users who have acquired the installation media (because ISOs can be used to in-place upgrade a machine) do not install it until the patch exists.
At this point, there seems to be enough noise to suggest that there is a problem somewhere. Some speculation, as Jeremy mentioned, is that the drive clean-up (“Storage Sense”) process runs if the install process doesn’t have enough free space, versus simply failing the install. Storage Sense has been in Windows 10 for a while now, but the latest update adds the ability to remove local files if they are backed up in the cloud. Knowing the types of mistakes that programmers tend to make, it wouldn’t surprise me at all if Storage Sense didn’t have local files flagged properly, because the Windows 10 update hasn’t installed yet to state whether they were correctly migrated to OneDrive or not, so it got rid of them thinking that they were online.
This is complete speculation on my part, though!
You can then go into how sketchy it is to have files automatically removed from a device’s storage given that online storage services do occasionally lose files. The feature can be turned off in the Settings app, however, under the System -> Storage category. I don’t know if that will fix the upgrade problem, however.
For now, stick on the April 2018 update until Microsoft says anything. Personally, I'll install the new version on my new PC anyway (because it will have empty drives and it looks like this bug only affects the update process) but that's a bit of a risk.