caolan Technically you haven't quite asked a question, but you have made more of an observation, but regardless of my cheekiness I'll try to do my best to explain this phenomenon. * Note: I'm not a Dev, just a casual Solus user. *
If you've been using
eopkg and Solus for a while you will inevitably see this message pop up from time to time. Generally speaking this message can be safely ignored. But it's there to bring to your attention if it needs any further investigation, which in this case it does not. Most casual users will update from the Software Center, so they won't even ever see this message. And that's quite alright, the package still got downloaded, it still got updated, and it still got installed just fine.
But like you, I prefer to update through my terminal because I like to make sure everything gets downloaded and installed properly. I use the terminal because 1 out of 10 times eopkg may hang/freeze, which is not a big deal, I just have to quit it, restart it, and it'll resume downloading/installing where the cache last left off. Now getting back on track! The message saying the user probably deleted it is just the most common or most likely reason for why a file/folder may not be there. But with the case with some update, new packages may create new files or folders, which weren't there before so essentially a message like that will pop up. It doesn't require any input from the user, but more or less is letting you know that the above happened on your system.
It may be a little odd or jarring to see a line like that at first, but it's totally fine I swear! 😀