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The APS Catalog has been deprecated and removed from all Plesk Obsidian versions. Applications already installed from the APS Catalog will continue working. However, Plesk will no longer provide support for APS applications.
Please be aware: with the Plesk Obsidian 18.0.78 release, the support for the ngx_pagespeed.so module will be deprecated and removed from the sw-nginx package.
I don't recall anyone ever posting about that particular conf file being overwritten, but it's always good to have backups of all the possible conf files on server in any case.
And good to have a complete verified backup of any server before any type of upgrade/update, no matter how small it may seem beforehand...
Random chance will always find a way to bite one in the ***...
(Edit: Yes, Plesk *may* overwrite the file during an upgrade since they do re-package it with some mods in the conf file, such as specifying psacln as the default group ownership, and log file entries....) However, it looks like they may not touch the proftpd.include file...