the "Minion" forum would be best for Minion related questions.
Minion will always remove the total live/AddOns/<addonName> folder and then extract the new downloaded zip Archive with the contents of the newest versions. So the "/lib" and all other folders and files you have removed will be missing there as well.
That's another benefit compared to manually updating as most users simply "overwrite" the folder and keep old files and subfolders this way! if you manually update your addons you also need to remove the complete folder of the addon in live/AddOns/<addonName> before extracting the new zip archive manually. AND you need to make sure your archiving software (WinZip, WinRar, ...) does not create a new folder with the name of the zip file, but ONLY extracts the contents of the zip file (which will be the foldername of the addon, containing the txt and lua and maybe xml files of the addon + subdirectories etc.).
However, having heard that Minion sometimes doesn't properly apply updates I have to consider the possibility that this may be a reason for such reports.
Yeah, I've herad so many complaining and most of the time it's their antivirus tools blocking the access to the live/AddOns folder as it is located in your windows user directory! If you whitelist this in your e.g. Windows Defender and/or other antivirus and ransomeware protection tools it will just work fine.
The other reason this might error will be that Minion sometimes is not able to download the files properly and then it will hang.
In rare cases the zip files will be downloaded but only put into live/AddOns without extracting them, but the old addon folder was deleted properly already in live/AddOns. Clsoing Minion, deleting the minion cache/XML file often fixed this for me. But actually haven't had this happening since 3 years now.
Often Minion won't work if installed to the default dir as it is located in your user's AppData folder then! Installing it to e.g. c:\Minion or d:\Minion fixes this often. Same problem like with the Antivirus, you need to whitelist the Minion folder then or it got no access rights to write and read the xml, log and other files of the Minion cache.
If users got any other reports they need to report it here please, inclduding a description how to rebuild it and what they did (like antivirus whitelist etc.) and provide their minion.log and xml files like described in the "how to report..." thread here in the Minion forums please.