Preliminaries:

• Shopkeepers version: 2.18.0
• Spigot version: 1.20.1

HideFlags is originally 255 and will become 127 after being added.

Occurs after reboot

I think this is caused by the Spigot server converting these flags to signed byte (max value 127) in certain cases: https://hub.spigotmc.org/stash/projects/SPIGOT/repos/craftbukkit/browse/src/main/java/org/bukkit/craftbukkit/inventory/CraftMetaItem.java#880

I will propose an upstream fix shortly.

Upstream Ticket: https://hub.spigotmc.org/jira/browse/SPIGOT-7555

Pull request to fix it: https://hub.spigotmc.org/stash/projects/SPIGOT/repos/craftbukkit/pull-requests/1322/overview

A fix has been merged into the Spigot server. So rebuild the latest server version and try again.