How to deal with variations being removed in Woocommerce
Use the "In Stock" or "Out of Stock" option for each of the variations. Practically this means that instead of adding/removing variations all the time, you can simply update that variation. Going one step further, you could also hide "Out of Stock" items from the front-end by enabling checkbox found at WooCommerce > Settings > Products > Inventory > Out Of Stock Visibility.
Alternatively, if you're looking for a more "Spreadsheet-like" inventory management view, you could also consider using a 3rd party plugin like WooCommerce Smart Manager: https://woocommerce.com/products/smart-manager/