The problem is that Plesk doesnt honor package management when you use their microupdates (if you use yum you're good). So we are in fact doing it correctly, they just blindly ignore the systems configuration and clobber things.
While of course you are correct that it's bad that they're bypassing the package manager with their micro updates it's the users of the Atomic repository that suffer, because now they need to know about incompatibility between installing micro updates and a package in the Atomic repository.
We recommend you open a case with them to not do this, when they use rpm these things are taken care of automatically, but the microupdate system from PArallels doesnt. They've been scolded many many times, including back when Scott and I still owned Plesk that not do this. But some developers just don't care, so keep hounding them to drop this backwards system. They have a great package management system, they just dont use it for microupdates.
While I agree that Parallels switching to using the package manager again for their micro updates (they used to ship RPM's back when micro updates were still called hotfixes!) would be the ultimate solution and of course Plesk users should bug Parallels about this, it would be nice if it was possible to do something in the psa-proftpd package to prevent proftpd from breaking. I'm sure Atomic users and ASL customers would like that.
After all Atomic is upgrading one of the Plesk packages here with a modified version and I can very well understand that maybe Parallels won't support people who do that. Or is it really just impossible to prevent micro updates from breaking the Atomic version of psa-proftpd?
Anyway, this FAQ is the simple procedure to fix their poor package management:https://www.atomicorp.com/wiki/index.ph ... sl.conf.27
Which is just to run this command as root:
yum reinstall psa-proftpd psa-proftpd-xinetd
Sadly you'll have to run that after every subsequent micro update, as all previous micro updates get reapplied when upgrading to a new micro update.