There is a limit on Shopify when merchant passes the 50,000 variants in total. https://d.pr/i/6TC65i
this limitation is not related to the Zonify app.
If you have more than 50,000 variants in your store, you are limited to import 1000 variants per day.
The only way to be able to import unlimited products to Shopify is to upgrade your account to Shopify plus.