settings.conf, these files are not meant to be edited by you. I will not give support or details for other configs, as creation and management of shops is supposed to happen ingame.
The income per player for the day are stored in
incomeLimits.conf to persist over server restarts. All shop transactions are saved in the
ledger.db.mv.db - you can inspect them with a h2 database editor. The database is never cleared at the moment so you may want to delete or trim it every now and then.
With that said shops are saved in per world configs by the worlds UUID. In case your world UUID changes you can rename the configs accordingly. Additionally every config creates exactly one backup when the server boots up.
Shop automatically save with the world, but can manually trigger a save at any time. This will not write any configs unless at least one shop was edited. Along with that shops are only loaded with a world. This means
/vshop reload does NOT reload shops from world configs - it only reloads the
AnimateShops Default: true
By default shops are animated, this means that mobs will periodically look around a bit. If you don’t want this behaviour for some reason, you can disable it here
AuditLogs Default: false
If you turn on audit logs VillagerShops will create a log file of it’s own, recording every action and interaction admins and players performed in vshops. This might help figure out if players are falsely claiming items gone missing or uncover admins abusing their powers and changing prices to their benefits. Because these logs might blow up rather quickly, this feature is disabled by default.
AutoDownload Default: false
In case you don’t want to bother downloading the translations yourself can enable this option (set to
true) to automatically download the translations from github.
For more information on how to use this, see the Setup Guide.
DefaultStackSize Default: full
This is the default selected stack-size for shops. Allowed values are full, half, quarter and single
NBTblacklist Default: 
You probably do not need this! The NBT blacklist is intended for any mods that do wired stuff with items once they get into playerhands or into containers. Use an NBT viewer like
//NBT in Mike’s ToolBox to figure out these information. Every entry (and
sub entries) in this list will be removed from ItemStacks before they are compared.
Path elements are separated using slashes. If that turns out to be a proble please report back.
Also it would be aswesome if you could tell me about any other troublesome NBT Tags you found.
SmartClick Default: false
For shop items that have only either a buy or a sell option smart click will allow right and left click to perform the single available action. Otherwise left click will always buy and right click will always sell.
VersionChecking Default: false
Enabling this feature will check for updates once, when the server starts. It’s strongly recommended to enable automatic version checking, This will also inform you about changes in dependencies.