What happens to my extra store locations if the Multi Warehouse plugin is deactivated?

No. Nothing is deleted. Without the plugin, the limit only stops you creating new records once you already have one of that type. Viewing, editing and deleting the ones you have still works.

What you will notice:

• On Territories and Store Locations, the + Add button is replaced by Upgrade to add more, with a note that your plan includes one for free.
• The Multi Warehouse & Store page shows counts like "4 / 1 free" and Free limit reached instead of "Plugin active — unlimited".

Reactivate the plugin to add new territories or store locations again.