Shopkeepers Version: 2.23.3
Spigot Version: 1.21.4-R0.1-SNAPSHOT

Not so much a bug, just some help migrating.
Shopkeepers Version: 2.23.1 > 2.23.3
Spigot Version: I don't know and neither do they > 1.21.4-R0.1-SNAPSHOT
Minecraft Version: 1.21.1 > 1.21.4

Save File: save_before_before_2.txt
Error Message: Caused by: java.lang.IllegalArgumentException: Specified class does not exist ('FoodEffect')

Changing all of the (3953) to (4189) doesn't fix it.

What are the steps to update the current Shopkeepers settings to work in the newer versions?

In MC 1.21.2 the "food" item data component was changed (certain properties such as food effects were removed) and a new "consumable" component was added. However, there is no automatic conversion of the previous food effects to the new consumable data (Spigot simply removed support for loading the previously saved food effect data).
And support for the new "consumable" component wasn't even added to Spigot until a few days ago.

Your save file seems to contain a lot of items with custom food effects. You will need to either remove those food effects / items, or update your server to the latest version and somehow manually convert this serialized data to the format of the consumable component data.

However, I will not provide help with that (there is no easy way for the Shopkeepers plugin to automatically migrate this data either).

If you attempt to manually convert the data to the new consumable format, you can get information about how this consumable data is saved to disk by preparing an item with a consumable component and effects in-game and adding it to a shopkeeper and then inspect the save file, or using the /shopkeeper yaml command while holding the item in-hand.